You may think that 'nihongo-wo yoku wakaru' is more natural, because nihongo is not the subject.
In the same way it seems more natural to say 'nihongo-wo sukidesu' instead of 'nihongo-ga sukidesu'.
But we never say 'nihongo-wo wakaru','nihongo-wo sukidesu'.
I noticed this strangeness when I studied Korean. Korean has particles like Japanese, and most of them correspond one by one with Japanese, but in this case the usage is different between Japanese and Korean. Korean uses a particle equivalent to 'wo' in Japanese in these cases.
So, I think your doubt is very natural, and most of Japanese haven't even think about the strangeness.
I don't know exactly why we use ga/wa when we say 'nihongo-ga/wa wakarimaru' and not say 'nihongo-wo wakarimaru', but anyway we say like that.
I'm not sure your question is the choice between ga/wa and wo, or between ga and wa.
In this case, you can use both ga and wa. Ant the difference of meaning is like below.
'Anata-wa nihongo-ga yoku wakarimasu ne' You understand Japanese very well.
'Anata-wa nihongo-wa yoku wakarimasu ne' You understand Japanese language well but...' this implies negative things such as you don't understand other languages, you don't understand Japanese culture, you can't play the piano....'