3CSR7.410(1G) states: "Firearms may be used to take wildlife...Except for hunting deer, any shotgun having a capacity of more than three (3) shells must have the magazine cut off or plugged...so as to reduce the capacity to not more than three (3) shells in the magazine and chamber combined."
3CSR7.431(5D) states: "Prohibited in use or possession:...2. Self-loading firearms with capacity of more than eleven (11) cartridges in the magazine and chamber combined."
These are the regulations you refer to in your question. As I understand it, the reason for a three shell limit in shotguns goes back to when pump action shotguns were first manufactured. Traditional over/under or side-by-side shotgun hunters of the time felt the increased magazine capacity gave hunters using pump guns an unfair advantage. Federal regulations limiting waterfowl hunters to shotguns capable of holding no more than three shells were enacted.
The limited magazine capactiy refers to semi-automatic (self-loading) firearms used for deer hunting. If you are deer hunting with a shotgun with slugs, you can take the plug out (remember to put it back in before you go bird or small game hunting!). If it is a pump, lever, or bolt action, you can have as many slugs as you want in it. If it is a semi-automatic, you are limited to total capacity of eleven (11) in the magazine and chamber combined. The same rule applies to rifles and handguns used for deer hunting. This is a safety measure.
Please contact your local Conservation Agent for further clarification or explanation.