I'm upgrading the missus' Commencal from V-brakes to Avid Juicy 3s but her hubs are Shimano centrelock, am I alright to use Shimano centrelock rotors? Will there be any compatibility issues?
Yes. No
Some of the high-end Shimano rotors with the big spider will foul on the pad tabs, however you'll be fine with the cheaper ones.
The cheaper ones can often only be used with resin pads though. You can also buy 6 bolt adaptors if you want to run 'normal' rotors.
why can the cheaper ones only be used with resin pads?
I'd bought a pair of the C/L rotors before noticing the 'resin pads only' marker.... I only paid £15 for the pair, so thought "what the hell" and stuck them on with my Juicy 3's..... 8-9 months later and a few sets of semi-organic pads, and they look no more worn than any other disc's I've used, and they seem to perform spot on too.
They seem pretty soft, and also rust if you leave them outside all the time, so I guess using sintered pads (not semi-organic) pads would wear them down.
mine fouled the brake tabs so I cut 'em off and now they work fine.
For what its worth I am running an XTR splined rear rotor with a Magura Louise caliper - no issues here.