I think it should be safe to apply the shrinkwrap modifiers if they have served their purpose. With any modifier it’s important to keep in mind that the modifier is doing some work on the mesh so the mesh itself is not being permanently changed. Applying the modifier will make those changes permanent so there is no going back after it’s been applied. Worst case, make a copy of the mesh and apply the modifier to only one of them so you can revert to the unapplied version if something goes wrong.
For my workflow, I avoid texturing and unwrapping until “Stage 1” of rigging is done. “Stage 1” gets me to a point where the main body of the character is rigged and weighted. This allows me to transfer weights to clothing, (huge time saver) avoids having to redo any unwraps if the topology of the mesh is not allowing good deformations, gets the most out of the Rigify rig before any customization of the rig is done.
For your project, I still think using mesh deform modifiers and a deform cage for both clothing and body may be the best route to go. The meshes that make up the shirt, hand wraps, pants, etc will have very different topology and that makes weighting them to deform correctly very tough. Using a deform cage, every mesh will be bound to the same cage and will deform equally, despite having different topology. This method is a little advanced so it can be a bit harder to accomplish if you’ve never rigged before.
Good luck!