What is the logic behind the bean cards to be removed from the deck in Bohnanza?
It seems clear that the very valuable, very scarce beans will work best when there are neither too many nor too few players at the table.  With too many players, these beans are too hard to make work: if you take a risk and plant one, at a competitive table you may never be allowed to plant another!  Conversely, with too few players, these beans are too easy to make work: you stand a good chance of just randomly drawing into them on your turn and making a killing.

I suspect the Coffee Beans exist to make up the numbers in games where the Cocoa and/or Garden beans have been removed.  They are a pretty generic bean, plentiful and of low value, unlikely to rock any boats.  I don't think the Coffee beans would be unbalanced in a 3/6/7 player game in and of themselves; but they need to be removed just because, if you'll allow me to mix my metaphors, too many beans spoil the broth.  The more types of bean you have in the mix at any one time, the more random the draws become, and the less easy it is to discern a hopefully optimal strategy.  (Equally, of course, too few beans makes it too easy to see the "best" plays.)

Keeping the number of beans in play down to 9 or 10 at any one time keeps it easy, but not too easy, to wrap your head around the numbers of what's going on.  If you just want a fun, random, noisy bean-collecting game where you don't really care about the finer points of game balance or cutthroat competitive strategy, I'd suggest that it's probably not worth your while removing and adding different types of beans between every game.  Depends entirely on your motivations for playing Bohnanza!