Aha! If you have Indonesian citizenship, get Indonesian passport
It seems that it would be difficult for him to have an Indonesian passport,
at least legally. He came for the first time in Indonesia in 2000 and is born from a foreign father. Back in year 2000, the citizenship law of Indonesia (UU 52/1958 was the relevant statute at the time) was denying him Indonesian citizenship because citizenship was transmitted by the father and the father only.
As a consequence, it is very probable that his mother made an "arrangement" with either his birth certificate or any other document so that he can stay here without too many question being asked. This is in this case an important notion to grasp because Kanmaro may suffer the consequences of it now, eventhough he has no guilt in what has probably happened.
Unfortunately quite a few kids have been in similar situation, some having their birth certificate rewritten or modified so that a different father or no father appear on it. I know a couple of case in my circle and I suspect that there are much, much more than just a few if we consider that I am personally aware of two just in a small city than the one I live in. Detailing here these two cases would probably stunned most foreigners who are used to a different type of Administration that we got here.
This kind of "arrangement" has had a consequence on these kids when in 2006 the Citizenship Law of Indonesia has changed. It has simply bared those kids to access dual citizenship. Difficult for the mother to go the Kanwil and say "I would like my son/daughter to have dual citizenship as per the law but here is what I did..."
I understand that Kanmaro may not want to go into too much details and want to be cautious. If he does have an Indonesian passport, expired or not, the legality of said passport may be seriously questioned considering what I said in my paragraph 1 and if, as I suspect, the mother has never applied for dual citizenship for him.
I have been proposed a KTP WNI in the past, and so did a couple of foreign friends of mine. If I would have accepted it, it wouldn''t have made me Indonesian legally despite having a KTP WNI to show. A friend accepted a KTP WNI and I hope he is not foolish enough to believe that he is Indonesian legally just because he has a KTP WNI. The fact that Kanmaro may (or may not) have an Indonesian passport does NOT make him a LEGAL Indonesian citizen. This is where the trick is.
Whatever Kanmaro decides, flashing Indonesian documents to officials is perhaps not wise and may have his mother in trouble. It all depends on what she has done for him to come and stay in Indonesia while he was obviously not entitled to Indonesian citizenship being born in 1994 (arrived in 2000 at the age of 6 y.o as per the OP's post) from a foreign father.,
To answer one of Kanmaro's question: Imigrasi can not fine you at all. If you are legally considered a foreigner, your overstay is far too long for you to be liable of a fine.