No idea why NT implemented a limited money system honestly, but yeah you're limited to 10K zeni (9999 ackshully but yeah).
Fwiw money isn't hard to make once you get Chi-Chi. Just talk to Mai disguised as Shu while playing Oolong and you get a big wallet which extends your max funds to 9999. Then play as Chi-Chi during the evening in the desert, and go digging. You'll fill up in no time.
Also off topic, that image above reminds me I colored this image last month. I offered help to NT to do placeholder colors until he can get to it but I guess he wants to do them himself, so I'll just post it before I delete it off my hard drive.