My girlfriend and I have been uin an apartment for nearly 5 years, have kept the place very clean, but after that much time, the cheap carpet is of course, even cheaper and will need replacing when we leave. The paint is still the same color, we will be cleaning them.

My question is :After nearly five years, can they deduct the costs of replacing the carpet/painting from our deposit?

Simple answer, yes.
Now it really depends on what they class as fair wear and tear over this period.

If in any doubt challenge the landlord/agent to explain their calculations.