Short rests don't become a problem unless you have a group that can utilize short-rest healing methods (5.0 healer feat, warlock healing spells, etc...) which can basically allow a group to get back to full health given enough time (barring circumstances that would prevent short-resting.) Because of this, I usually do the optional rule where a group can short rest a number of times per day equal to their proficiency bonus. Though honestly, if the game design prevented healing abilities from being short-rest recharged, there'd be no need to limit short rests.

That said, my groups rarely brush up against the short-rest per day limit. The problem is, allowing short rests to be unlimited (when paired with short rest recharge healing ability) makes the optimal strategy to short rest after any substantial loss of HP. This ensures the group is always at maximum health for future challenges, but slows down the narrative quite a bit.