Sure, a two-byte money counter is doable, and not very hard, but I wonder if it is THAT relevant. I did plenty of playthroughs of this game, and the time I spent farming was minimal at best. However, knowing the secrets that give money ("It's a secret to everybody") help a lot. The big expense is the Blue Ring, and I think it's fair to make it hard to obtain. Having a limit of 255 rupees means that you can't accumulate past that point, so in a way, you're forced to be economical at some point after finding the actual secret store where the Blue Ring is sold. Having a limit of, say, 999 rupees would make it too easy to just accumulate like crazy through normal fights (i.e. not even trying to farm) and soon enough, any expense is like pocket change.
Just my two rupees...