Will I have to adjust my email client configuration to use my private machine's mail server directly or is it possible to still use imap.ionos.de and they will take care of routing to my local machine which is provided in the MX record with my DynDNS domain?
They will not take care of any routing, because there's no actual relationship between your MX records and accessing mail via IMAP. (Many larger providers have completely different sets of servers.) Even sending mail from your client via SMTP still does not use the MX records of your domain; the only purpose of MX records is to tell other domains how to deliver mail to you.
Even if IONOS did know which servers you use for IMAP and outbound SMTP, this is still not a service that hosting companies offer. If you want your email client apps to use imap.example.com, you will have to configure them to use imap.example.com yourself.
Am I going to experience major blacklisting and spam flagging issues after having those set up or will my mail address still be whitelisted since it routes through imap/smtp.ionos.de?
What you described does not cause mail to be routed through imap/smtp.ionos.de at all. (Outbound mail delivery doesn't even involve IMAP.)
When you run your own mail server, its default mode of operation is to deliver outbound mail directly to the recipient (using the recipient's MX records). With most recipients you will indeed have issues trying to do this from a residential Internet connection – assuming your ISP even permits outbound SMTP connections at all.
Unlike in the previous section, relaying outbound mail through IONOS or another provider may be possible (and would avoid the "residential connection" issues to some extent), but the configuration for that would be done within your SMTP server's settings (e.g. "relayhost" or "smarthost") – not through DNS.
If you're still considering running the server yourself, either run the whole mail server at a datacenter, or run the primary server at home but configure it to send everything through a "relay" server at a datacenter (your own or IONOS if they offer that service) – but I would suggest to only do this after you've figured out the differences between SMTP and IMAP.
