"But Japanese has over 10.000 or something like that Kanji with no real order."
As much as I know . is used as a number separator in many European languages that still amuses me every time.
But yes it might well boil down to hand encoding every character.
Some things to try before that
The same devs would also face the problem of however many thousand characters they need and would also not want to hand type everything.
To that end
http://www.rikai.com/library/kanjitables/kanji_codes.sjis.shtml and
http://www.rikai.com/library/kanjitables/kanji_codes.euc.shtml and other common standards might have their order or even outright encoding borrowed -- plenty of Japanese games have been seen to have the shiftJIS setup from 8000 onwards in there but omit the first part).
Most common/least common in the text has been seen.
Order used in the text has been seen. The reverse could also be possible.
Same order as in the font has been seen many times.
Do also be aware that the above three may have been done for an earlier version of the script while it was still in development and thus be different from the final. Does not happen often but can happen.
In the case of fonts then the nftr font format used in many DS games does not have the encoding in it but it will have the character able to be displayed along with the value that calls it. NFTReditor will be able to help you here.
Japanese is taught in various levels, get a popular way it is taught in schools or something (joyo kanji being a good start) and it might match that. If you have a Japanese speaker/native/one that might recognise this sort of thing then yeah.
The developer may well have previous format it used. I normally see the English one but Capcom have a nice table that matches the lower case Roman characters with the upper case ASCII, but it otherwise very custom.
I have never seen anybody successfully use it in anger but there are some tools that attempt to OCR (texterkennung if my dictionary has not failed me) things and are aimed at hacking. Crystaltile2 is the most well developed but it is not good, not to mention is seems to be based around Chinese and that does not play so well for Japanese.
Do also remember you have the game in front of you and if it is for a nice system you can easily run modded games for then you can play with it. For instance if you found where the text is in the game (corruption, names, assembly tracing... does not matter really) you can then put any value you like in the text section, or any run of characters or something else that might reveal something far quicker than a weekend of static analysis.
Beyond that even much like I have not typed the character z before now then not every script will use every character -- you might only need enough to decode a section, or the whole script, or enough of it, for your translation to be getting on with.