The water in the bilge is not, to me, a big issue at all. As mentioned, these boats will let water in. With the boat on the hard, it means it's just rain water and, while you would want to limit it as much as possible, it's presence is not that big a deal.
However, the fact that you mention the soft spots is a concern. I've seen a lot of "small soft spots." They all have two things in common:
1. They're not really small
2. The core will be rotten: by the time the deck flexes, the core has turned to mush.
The fact that there is enough moisture in there to crack the deck when it freezes should tell you all you need to know.
That said, core repair is a very doable DIY job. Not a small project by any means, but it's certainly manageable assuming the core damage is not pervasive. Just know that you will need to remove the top deck skin, excavate and replace the core and repair the deck. If a broker or anyone else tells you that you can repair it by drilling a bunch of holes and filling them with epoxy, then they're misinformed.
