So in the new SR 5 rules my deck is going to get fried a lot, it's going to happen. They say just to 'repair it' and the B&R skills tell me how that's done.

But where are the costs of repairs? I mean seriously, the way it's written the rules seem to assume if you want to repair something you have what you need. Doesn't it cost a certain amount of nuyen per box you fix or something?

I haven't seen anything telling how much it costs but you could use the rules from SR4 in Arsenal for repairing vehicles where it costs 1% of the base cost of the device per box of damage. However, the matrix or rigger section (can't remember which off hand) in SR5 seems to talk about it being more expensive to repair stuff than just buying new.