Does the size of the cap booster affect the shield boost bonus?
Solution 1:
Nope, the size of the charge has absolutely no effect. Always use the smallest possible charge for Ancillary Shield Boosters.
Solution 2:
It does not matter which size of the Cap Booster charges you use, but there is a difference between regular and Navy Cap Boosters. From the Retribution patch notes:
Reduced capacity – 7 regular booster or 9 navy boosters.
So you should always use the smallest charge that fits, and preferably the Navy version unless you're on a very tight budget.