I voted " Limited by something else".
Since you can hardly predict party composition and tailor the entire game for all possible classes combinations I think the best solution is simply to have it as it is right now ( 2 uses + virtually unlimited long rest) and restricted in some areas with prior info for player how his ressources should be distributed.
" We won't be able to rest if we go there until we do X,Y,Z and Z is the ultimate goal/boss whatever". If you decide to leave you" fail " the quest in a way with no possiblity to come back for instance. A " localised " sleeping denial creates a closed environment you can control and balance with relative ease to not be a " brick wall" impossible to go throught for some party compositions. You avoid a game with a " dead end" with no possible solution. And yet you reward good ressource management in the light of this closed environment. In this particular case you can adjust the encounter to the existing sleeping mechanics(Only short rest, no long rest for instance).
On the scale of the entire game however .... how do you want to limit short rest? On what basis? You can short rest 6 times? 20 times? Why not unlimited? You can't have arguments for or against in a situation where you simply do not know what challenges the player will be facing at a given time. The resting systems replenishes player's ressources so he can deal with the challenge on the map. The player currently can sleep virtually endlessly because all challenges on the map (if put together) are infinitely outclassing a 4 men party capabilities. And you don't know in what order the player will approach them. You have a limited control over starting ressources(Level design is the answer here, obviously you can make it in such a way you will predict player's movement.But you will never cover all scenarios with level design. You can't create a dead end when the only solution is "reload and don't fail the roll this time").
I think you asked the wrong question. Instead of asking " Should short rest be limited?" I would rather say " Should resting be limited?". In that case I provided the answer above. I hope we agree for the most part.
As far as Larian goes they seem to do it more or less this way.....only they aren't implementing the long rest limitations even for the biggest battles. Instead they implement " very big battles" as a culminating ressource management test.
Example:
Goblin camp assault or Druid Grove assault should be 100% a case of no long rest until we get rid of X,Y,Z[We need to open the gate, get our soldiers in and seize control of the main druid lair]. If you leave the battle vicinity prior to accomplishing the final goal you could be issued a warning and if you make the explicit choice to leave the battle should default to a pre-defined end and the player should face the consequences of his actions. Wheter positive or negative is a matter of personal preference of the quest designer.
Such a fight would be the moment to use the items you found + scrolls to overcome potential failed rolls on spells or defensive rolls. A success should have extra flavor. Even if only partial( player opens the gate, get Minthara's troops in the Druid grove but gets rekt so badly he decides to leave the battle and long rest. As he comes back Minthara is salty but despite her losses you still got her in and she can't deny it.
Voila voila.
