Or Does it create any problems to give my employer the NL IBAN of Bunq?
No. I use my NL IBAN for many years now, and I live and work in Germany.
Are there are any fees regarding this kind of transfering money between countries?
No. SEPA transfers cost the same whether they're sent domestically or internationally. Both Germany and The Netherlands are inside SEPA and all banks normally use SEPA transfers to send money between accounts and for wage payments.
I don't know if it's related, but I'm not even an EU citizen.
Unrelated.
Currently i don't have a permanent address in germany and cannot create german IBAN.
Actually at bunq (just like the user Marek above me mentioned) you can still create an account with German IBAN even if you don't live inside Germany. But it requires having the Easy Money or Easy Green plan. Then you can choose "Bank like a local" > choose Euro as currency and then tap on the country of your choice.
However, even if you're on the Easy Bank plan and only have your NL IBAN account, there shouldn't be any issues with that in Germany. My personal suggestion would be to just keep using that account. I've been doing this for many years without issues in Germany.