Can i just put the NS records as the secondary DNS nameservers in the hidden primary zonefile ?
Yes. That is exactly how it is supposed to be done in fact.
Whatever is in SOA as MNAME is not relevant for normal resolution (only broken software look at it). It is sometimes the hidden primary nameserver (see fr. for example) but even so it might not resolve or resolve but not be available.
Note that primary/secondary is kind of useless terminology. It is not something visible from outside, from clients requesting data. The only thing that matters is the NS recordset that must match between both sides of the delegation cut point. For the outside querying clients, all nameservers listed in the NS recordset are the same and all are supposed to have a complete copy of the zone content, no matter how (between one of them being primary and other feeding them from it, or all of them feeding from another one not present in the NS recordset).
The hidden primary DNS service provider is requesting to setup vanity NS in the zonefile
As you don't give a lot of details, you might want to just ask more to your DNS provider and understand what they want because obviously you depend on them.
