Why are almost all STOL aircraft high-wing?
You're correct that the low wings produce more ground effect compared to their high winged counterparts. However, during takeoff and landing, it can result in undesirable handling qualities- the aircraft can 'float' the runway; on contrary, the high wing design is more stable. There are other reasons for STOL aircrafts to have high wing designs, most of which has to do with the location of their operation, as you noted:


Most of them are operated from austere airfields. The high wing location gives some protection from the debris (and obstacles).
For the same reason, engines mounted on the high wings have better protection compared to the low wing mounted ones from FOD ingestion.
Most STOL aircraft use large TE flaps. In case a low wing is adopted (and also if propeller is used, like Twin Otter, for example), the required ground clearance will require long and consequently heavy landing gear. This can be avoided in case of high wing design.
The visibility is better compared to low and mid wings.


Historically, STOL aircraft have been high wing. Also, some of the STOL aircraft are (military) cargo aircraft- the high wing means there is no wing spar across the cargo compartment; plus, the low fuselage means easier loading/unloading of cargo.