I just went through this, had water coming in for YEARS at the stuffing box area, last year to the tune of 5 gallons every 24 hours.
My yard fixed the structure around the shaft at the stuffing box area.
Yes your keel has water in it (most of them do), as the keels were weighted with concrete (which is porous by nature depending on the yard that mixed it and poured it). Mine leaks out the rear of the keel when out of the water also.
My .02... fix the leak inside the boat, I just laid out $1500 for the glass work around the shaft log area. I know there is water in the keel... but knowing how it was built... I know a guy who took a grinder to his keel wherever he found water seepage. It was a never ending task. After weeks of grinding and fiber glass repair, he gave up. If the water doesn't get in the boat...