i couldn't give you a fixed % as there are too many factors to take into account, range being foremost among them.
very long answer:
assume the shooter to be on the left, the intended shot to be along the adjacent, and the actual shot trajectory to be along the hypotenuse.
in this example, you can see the difference that it makes, and you can see that in this case, at these ranges, the shot will miss both the small and the large target. however:
same shot deviation, same enemy sizes, transposed distances. the larger unit would be hit, and the smaller unit would be missed by a large margin.
again, same setup as before, but in this case, it would hit both targets because they are closer, so the deviation has less of an effect.
note that all these examples are given in 2d form as viewed from directly above, with the deviation taking place purely in the lateral plane. shots also deviate vertically.
any given shot can deviate by any given angle, and the smaller or further away the target the greater the chance this deviation will cause the shot to miss. but the chance to deviate, and the angle of deviation can be thought of in terms of a constant when comparing two shots. in this respect, it is no harder to score a shot that deviates very little against a thin target than it is a thick one. remember that there are multiple calculations taking place, the "to hit" determination effectively dictates the multiplier for the amount of POSSIBLE deviation, which is fairly random. if the shot is good, it's good. however if the shot DOES deviate, the angle of deviation required for a shot to miss a thinner unit is shallower.