MySQL performance issue due to caching

perl mysqltuner.pl --host 127.0.0.1

[--] Skipped version check for MySQLTuner script
[--] Performing tests on 127.0.0.1:3306
[!!] Successfully authenticated with no password - SECURITY RISK!
[!!] failed to execute: SHOW SLAVE STATUS\G
[!!] FAIL Execute SQL / return code: 256
[!!] failed to execute: SHOW SLAVE HOSTS\G
[!!] FAIL Execute SQL / return code: 256
[OK] Currently running supported MySQL version 10.4.17-MariaDB
[OK] Operating on 64-bit architecture
 
-------- Storage Engine Statistics ---------------------------------------------
[--] Status: +Aria +CSV +InnoDB +MEMORY +MRG_MyISAM +MyISAM +PERFORMANCE_SCHEMA +SEQUENCE 
[!!] InnoDB is enabled but isn't being used
[OK] Total fragmented tables: 0
 
-------- Analysis Performance Metrics ---------------------------------------------
[--] innodb_stats_on_metadata: OFF
[OK] No stat updates during querying INFORMATION_SCHEMA.
 
-------- Security Recommendations ---------------------------------------------
[--] Skipped due to none of known auth columns exists
 
-------- CVE Security Recommendations ---------------------------------------------
[!!] CVE-2021-27928(<= 10.4.17) : "A remote code execution issue was discovered in MariaDB 10.2 before 10.2.37
[!!] 1 CVE(s) found for your MySQL release.
 
-------- Performance Metrics ---------------------------------------------
[--] Up for: 2d 20h 44m 2s (48K q [0.196 qps], 384 conn, TX: 885M, RX: 18M)
[--] Reads / Writes: 99% / 1%
[--] Binary logging is disabled
[--] Physical Memory     : 1.8G
[--] Max MySQL memory    : 46.5G
[--] Other process memory: 0B
[--] Total buffers: 8.3G global + 258.9M per thread (151 max threads)
[--] P_S Max memory usage: 0B
[--] Galera GCache Max memory usage: 0B
[!!] Maximum reached memory usage: 11.3G (617.92% of installed RAM)
[!!] Maximum possible memory usage: 46.5G (2537.09% of installed RAM)
[!!] Overall possible memory usage with other process exceeded memory
[OK] Slow queries: 0% (0/48K)
[OK] Highest usage of available connections: 7% (12/151)
[OK] Aborted connections: 1.30%  (5/384)
[!!] name resolution is active : a reverse name resolution is made for each new connection and can reduce performance
[!!] Query cache may be disabled by default due to mutex contention.
[!!] Query cache efficiency: 19.8% (11K cached / 56K selects)
[!!] Query cache prunes per day: 7584
[OK] Sorts requiring temporary tables: 0% (1 temp sorts / 9K sorts)
[OK] No joins without indexes
[OK] Temporary tables created on disk: 14% (1K on disk / 10K total)
[OK] Thread cache hit rate: 80% (73 created / 384 connections)
[OK] Table cache hit rate: 99% (74K hits / 74K requests)
[OK] table_definition_cache(400) is upper than number of tables(77)
[OK] Open file limit used: 0% (48/32K)
[OK] Table locks acquired immediately: 99% (5K immediate / 5K locks)
 
-------- Performance schema ---------------------------------------------
[--] Performance schema is disabled.
[--] Memory used by P_S: 0B
[--] Sys schema isn't installed.
 
-------- ThreadPool Metrics ---------------------------------------------
[--] ThreadPool stat is enabled.
[--] Thread Pool Size: 1 thread(s).
[--] Using default value is good enough for your version (10.4.17-MariaDB)
 
-------- MyISAM Metrics ---------------------------------------------
[!!] Key buffer used: 18.2% (24M used / 134M cache)
[OK] Key buffer size / total MyISAM indexes: 128.0M/0B
 
-------- InnoDB Metrics ---------------------------------------------
[--] InnoDB is enabled.
[!!] No tables are Innodb
[--] InnoDB Thread Concurrency: 0
[OK] InnoDB File per table is activated
[OK] InnoDB buffer pool / data size: 8.0G/0B
[!!] Ratio InnoDB log file size / InnoDB Buffer pool size (1.171875 %): 48.0M * 2/8.0G should be equal to 25%
[OK] InnoDB buffer pool instances: 8
[--] Number of InnoDB Buffer Pool Chunk : 64 for 8 Buffer Pool Instance(s)
[OK] Innodb_buffer_pool_size aligned with Innodb_buffer_pool_chunk_size & Innodb_buffer_pool_instances
[OK] InnoDB Read buffer efficiency: 100.00% (609465732 hits/ 609485088 total)
[!!] InnoDB Write Log efficiency: 88.45% (3109 hits/ 3515 total)
[OK] InnoDB log waits: 0.00% (0 waits / 406 writes)
 
-------- Aria Metrics ---------------------------------------------
[--] Aria Storage Engine is enabled.
[OK] Aria pagecache size / total Aria indexes: 128.0M/0B
[!!] Aria pagecache hit rate: 94.9% (28K cached / 1K reads)
 
-------- TokuDB Metrics ---------------------------------------------
[--] TokuDB is disabled.
 
-------- XtraDB Metrics ---------------------------------------------
[--] XtraDB is disabled.
 
-------- Galera Metrics ---------------------------------------------
[--] Galera is disabled.
 
-------- Replication Metrics ---------------------------------------------
[--] Galera Synchronous replication: NO
[--] No replication slave(s) for this server.
[--] Binlog format: MIXED
[--] XA support enabled: ON
[--] Semi synchronous replication Master: OFF
[--] Semi synchronous replication Slave: OFF
[--] This is a standalone server

One of our production server has some performance issue, I have found that it was mostly related to MySQL, and after running MySQLTuner, I have found a few things of interest. Surprisingly, there's no join without indexes, so I don't think I can do much and it seems to be due to caching, and I know we're using W3T Total Cache, but I don't see any config except general ones in the WP admin panel, so I am wondering if there are ways I can cache more queries, because only 20% of them seem to be cached for some reason. And the query cache prunes are way too high, so I am wondering if I understand those metrics correctly and I could prune less of them every day to be able to cache at least 40%. Also, I am thinking increasing RAM could help our server, but that's almost a different issue.

These seems to be the most relevant:

[!!] Maximum reached memory usage: 11.3G (617.92% of installed RAM)
[!!] Maximum possible memory usage: 46.5G (2537.09% of installed RAM)
[!!] Overall possible memory usage with other process exceeded memory
[!!] name resolution is active : a reverse name resolution is made for each new connection and can reduce performance
[!!] Query cache may be disabled by default due to mutex contention.
[!!] Query cache efficiency: 19.8% (11K cached / 56K selects)
[!!] Query cache prunes per day: 7584

All your tables seem to be MyISAM tables. It is recommended that all table set up as InnoDB tables nowadays.

MySQL query cache is a deprecated feature due to various issues, therefore it is best to disable it.

After changing all tables to InnoDB, run MySQLTuner again and adjust InnoDB buffer pool according to its recommendations.

You must also upgrade your MySQL server, since your version has an open vulnerability.

I suspect that swapping is the real problem. You have over-committed RAM. Here are the things that jump out at me:

Physical Memory     : 1.8G
InnoDB buffer pool / data size: 8.0G/0B
Highest usage of available connections: 7% (12/151)

After switching to InnoDB and turning off the QC (as Tero recommends), make note that your RAM is too small for the given innodb_buffer_pool_size.

More specifically, make these configuration changes:

innodb_buffer_pool_size = 500M
max_connections = 30
query_cache_type = 0
query_cache_size = 0
key_buffer_size = 24M

If you still have issues after making those changes, start a new question in dba.stackexchange.com; it is a better forum for MySQL/MariaDB configuration.