Were there worries about a rebellion or something if the local population was armed or materials were stockpiled there? Couldn't they have just paid for warehouses and sent World War I surplus and other older equipment to the Philippines?
Not really.
The problem is that the Philippines are in the tropics. The heat and humidity played hell with everything. You could do okay with rifles, as long as they weren't used (cosmoline is great at that, but you can't use a weapon that is literally packed in grease, even then the wooden cases would get eaten by the bugs).
Ammo would deteriorate, as would other explosives. Cans would rust. Wing fabric covering would rot or be consumed, wooden wing spars would warp, the weather destroyed everything. Clothes would rot in the wrappings. You need climate controlled spaces in the tropics to store almost anything. That didn't exist, at least not a reasonable cost, in the 1930s.