Yeah, it's a nice alternative to Teeheespresso-farming, IMO; you can buy them for ~500 and 1,000 coins (I think) towards the end of the game. However, beans are also easier to come by after getting the Game Boy Horror SP; enemies in the Beanbean Castle Town outskirts drop all four types.
And the Mush Badges aren't totally removed, but the only "Shroom Force"-inducing badges are boss-drop-exclusive, and the two bosses that have them are very late in the game. Again, they don't do much against the final boss anyway.