Does VDD_3.3V at P9 Expansion impact other function?

Q1: I connect a wifi module on BBB, it using VDD_3.3V on P9, and my power jack can’t boot my board. But USB can boot.
Q2: In BBB ref I saw Ethernet(RJ45) using VDD_3.3VB. If I using VDD_3.3V on P9, will it impact RJ45 working? (Now I can’t connect two BBB by RJ45 & PLC)

Not that I know of. The VDD_3.3V on P9 as you call it is VDD_3V3B. Using that volatge should not effect the RJ45, but depending on your design, other things could cause issues.