basically, yes. but it has nothing to do with the ps2 version.
The first PS2 release (plain MGS3) didn't use the right analog. the second PS2 release (Subsistence, also in the HD Collection) only uses the right analog for moving the camera around Snake in third person. Aiming is on the left stick, which means you can't move and aim like a standard third person shooter.
MGS4 changed it to left stick = move, right = camera/aim. Peace Walker had more or less the same scheme but had to use the face buttons to aim since it didn't have a second stick.
iirc, the MGS3 on 3DS uses Peace Walker's controls where you aim with the face buttons. It actually adds some MGS4/PW mechanics like moving/aiming, third person aiming, and crouch walking.
It'll make a bigger difference in MGS3 3DS than RE:R. Realistically, unless other aspects of the port of a mess, the MGS3 w/circle pad pro would control even easier than the MGS3 on PS2.