It would be hard to use a jig to drill straight with the keel still on the boat. I suppose telling what is straight w.r.t. the keel from inside will be harder too. I do not think you can trust that your cabin floor is perfectly square to the keel.
I think I'd drop the keel and fully inspect the bolts and only add new ones if there truly is a problem. If there is a problem, wouldn't you rather know than hope the extra bolts you added are enough? You are weakening your keel stub by drilling it up, maybe you will just make things worse?
Isn't that what happened to the Cynthia Woods? Poor repairs
to the keel stub after a grounding and maybe a design weakness resulted in the keel bolts ripping out of the boat. The bolts didn't break or come out of the keel, it was the boat that broke.