Hi
I wouldn't think it would cause a problem, or it already would have. The main issue I can see would be that of separation, given that your puter is a more viable editor and mixer. ie if they are already being summed into one output, it might be convenient for quick playing about, but when it comes to recording it cuts down on your mixing and production options by having them in the same stereo pair track.
What I would do:
Work out how to have the inputs of each instrument come into your PC and monitor your PC output (assuming your overall system lag doesn't cause issues), some sound cards do offer monitoring of the inputs to your computer bypassing loads of processing.
There is a possibility that your amp has a switch to control this "straight-through" behaviour. The whole point is to know why things are happening, so you can make them easily not happen when needed.