First of all, the supply depot being destroyable is a very heated debate. 2 hours of farming can be erased in seconds with a mortar or helicopter bombardment.
It makes it so that people are now starting to place arsenals instead of supply depot because atleast the arsenals are not destructible and holds 2100 supplies total. Which is less than 3000 but better than 3000 that could be destroyed anytime. So my first suggestion was to make it so that the supply depot are more tanky. Second suggestion is to be able to protect them from mortars and heli with some sort of building ? So that infantry can still shoot rockets at them and destroy the supplies.

And finally, when a supply depot eventually explodes. The building is still up ! So you need to dismantle it and rebuild a new one which is real time consuming.
Two options : 1) just make it disapear if it explodes. 2) Make it reparable with a repair truck and a shovel so that at least we don't have to replace the damn thing.
Option 2 is my favorite and if there is a way to quickly rebuild the supply depos I don't think you need to change the things I talked about in the first half of this issue report.

Edit : I forgot to say about the arsenals thing... And I think it is very important. Arma is a milsim. Supply depot should be the better option to stock supplies.
There is something very off about walking into a base and seeing 10 arsenals for storage. It brings me out of immersion.
It's an optimal strategy since 1.7 with the supply depot that can be destroyed.
Also if the supply depots are close to each other its start a chain reaction and every supply depots just explodes.
It's very cinematic (reminds me of squad a little) but it should not encourage player to just ditch them completly.