Are center lock rotors less likely to rub or resonate while riding than 6-bolt rotors?

Intermittent rub that corresponds to load received by the frame or fork doesn't have anything to do with how stiff the rotor or its connection to the hub is. It's the fork or frame being flexed, not the rotor.

Usually the issue is caused by the air gap between the rotor and pads being too little, such that flex that would otherwise go unnoticed is causing rub. Causes can include rotor truth, poor caliper centering, piston stickiness issues, crooked wheel installation, poor parallelism of pad surfaces in the caliper, and/or poor brake mount surface alignment. Sometimes one sees a situation where none of those problems exist but rub is occurring anyway from the rider simply overloading the bike, but that's not very common.

Center lock versus 6-bolt is not a factor. On QR disc bikes, the stiffness of the hub axle can be a factor, however. In particular, going to a thru-bolt hub is one way that rub under load can be mitigated in those cases where it's happening when all of the other potential causes have been pursued. Thru-bolts add stiffness to QR forks and frames.