@Jotne: I agree there are more ways to do it and each has some advantages and disadvantages. For now, lets focus on the presented issue that MNDP/CDP/LLDP is somehow passing through NAT. (which shouldn't happen under any circumstances - all these protocols work with L2 broadcasting so they should never be forwarded with L3 or even pass through NAT)
@easyspot: Personally I haven't notice such behavior on any of my devices but I am not trying to say that the issue does not exist. You described it pretty clearly, including serious consequences (packet storms).
I'll be happy to try it on same model to see if I can reproduce it in controlled environment. I guess we will need some packet captures, complete config exports (or suppouts), network maps etc... so we can prove it to Mikrotik staff. If it proves true, it would be pretty huge... Hopefully it is just some misunderstanding. (Is it possible that your pc is for example connected with wifi at the same time as cable, while wifi is on bridge-wan? Is it possible that you skipped some other relevant parts of your config?)