Should I consider [H+] as substrate in MCT transport equation?
To include or exclude the H+ basically depends on the scope of your model. The H+ can be used as external parameters if you assume that both sides of the membrane are well buffered and the pH will not change. If you want to simulate a condition during which the pH changes, like for example strong exercise in muscle or ischemia, then you would need separate H+ for each side of the membrane.