Some of these trucks are still being used heavily. Perfect example is that the Army Medical School (a regular Army unit) still have a large number. Considering the Maintenance Expenditure Level is zero on these trucks, units will be scrounging for the parts for fear of loosing the truck. In normal units, such as infantry unit, that might not be a problem since they can get loaned vehicles or get transport requests filled from other units. Since training units don't belong to the "same Army" as the field units, getting that support is significantly more problematic. So if a training unit looses trucks, they have a much higher potential of going without.
Tarps, bows, and side racks for trucks maybe turned in separately for a simple reason. These items are accounted for as a separate item from the truck. Think of it as a ring mount or a 50 cal or a S-280 shelter. Some folks that manage property will require it to be turned in separate from the truck (sticklers for regulation I imagine) while others write it off as a loss (which is one reason why the newpapers hears about how the military can't account for property).
It's hit or miss depending on time, location, and unit that turned the truck in. A recent thread discussed using vehicles as targets is a valid use of vehicles if it supports our war on terror. This concern that is raised here is similar if not identical. If stripping this vehicles helps out training troops, so be it.
Lastly, if the vehicle is stripped prior to going to GL, it's a situation of ensuring to inspect prior to buying.