It doesn't matter how deep they are as long as everything fits in. 20mm is a good starting point.
however deep they need to be to fit your pups and wires
Du Hast Meche

Member 21 of "I Survived UG Pwn Day"

Quote by HugoMadizon
What is a pup?

Quote by azn_guitarist25
sir, are you a retard.
Quote by Teleprompters
for strats it 5/8" i believe or thats what i was told

For a MIJ Strat, the PU cavity is precisely 5/8" deep and the pots cavity is precisely 1-1/4" deep. As I pointed out in your build thread, get the proper router bits and no matter how much those braces bother you, it is not OK, I repeat, it is not OK to route the cavities with your teeth!

Though it really doesn't mater unless you are using a see-through pickguard. You could go almost right through your guitar if you wanted to..... And besides. IF you don't route it deep enough the first time just try again!