Is it ok to use "Ja nai ndakedo na" / "Ja nai ndakedo" for emphasis/lamentations, for example
"demo jitsu wa wagahai wa nihongo go mada jozu ja nai nda kedo na"
"sore wa shigoto ja nai ndakedo!"

does it only mean "even though", or can it also mean something like "too bad/unfortunately" at the end of sentences - or does it always need a context to compare it to something?

Yes, it is OK to use "Ja nai ndakedo na " / "Ja nai ndakedo", but in this case, you had better complete a sentence just like " A Ja nai ndakedo na B" / "A Ja nai ndakedo B" (= even though ... not ..., B ), for example "(watashi wa) nihongo go ga mada jozu dewa nai keredomo... nihonjin to takusan hanashite mitai desu" , " shigoto ja nai ndakedo ... syumi de tudukete imasu." However, someone already said B in a certain context, you don't have to say more. The meaning varies to the context.
Pay attention! "...nai ndakedo" , "...ja nai ndakedo" are not really polite expressions although many people use them evey day. You'd better say, "...nai keredomo", "...de wa nai keredomo"

dillemme thanks!

Sorry for forgetting the translations.

(watashi wa) nihongo go ga mada jozu dewa nai keredomo... nihonjin to takusan hanashite mitai desu.
= Even though I don't speak Japanese very well, I want to talk with Japanese people more.

shigoto ja nai ndakedo ... syumi de tudukete imasu.
=Even though it's not my work, I love doing it. It's my hobby.