The second number, (R1-R4), denotes the color of the weapon/vehicle/etc.
The first number, (M1-M3), denotes the variant.
The EX and EXA skin are the same, but the EXA skin has more armor.
Despite the bullet velocities, and shapes, none of the pistols are meant for long range use.
There are no silenced weapons, as of 1-13-20, so if you are looking for stealth, this isn't it.
The second number, (R1-R4) does NOT have any effect on the utilities of the weapon, just the color.