You weren't specific if the gaps are splits in the wood or glue joints that have separated.

I would go along with the last thing you wrote. Yes, coat it. Sand it and coat it.
To fill splits or joints run a strips through the table saw and rip some thin strips of varying thickness like paper, then a little thicker etc. Plane and sand them to a "V" shape. That will take 5 minutes. Then glue them in where needed and they can sit proud. (stick up a bit) Sand them flush and coat the boat. Removing strips and fixing them is a lot of work and I don't think necessary. OK so the inside is not coated, what other choice do you have?

Good luck. Don't worry it will come out fine.