I agree with Jeff 100% for using washers inside the hull, under the nuts for the keel bolts.
In a completely "Outside the box" thought, you COULD use rubber washers, if the intent was to make the holes water tight in this fashion, although I can find no practical reason anyone would.
If this is truly for course work, and for theoretical use only:
One could use rubber washers, of a stable rtv silicone type, if the keel had shallow machined cavities for the washers around the keel bolts, where the cavity was designed so that the washer formed a slight compression seal around the bolt and the hull as the keel bolts were tightened from above. The cavity SHOULD NOT be machined into the hull, as this would weaken the hull under the nuts for the keel bolts. This whole process would be too labor intensive in practicality, but as an answer to a classroom question, that is how I would do it.