Normally I would tell people to dig a trench around their base for defense, but since you're near the water, you might not be able to dig deep enough. So instead, use your hoe and a whole lot of rocks and build an earth wall around your base. That will keep even trolls out.

For the bridge I usually use a single wood beam. Another option is to leave a small gap in your bridge that you can jump across. Trolls like to smash my balance beam, but it's easy to put back. For going over a wall or to a base that's on top of a rock, you can use a ladder or stairs that don't quite reach the ground so that you jump to get to it.

I have also been known to trench around a square area even if it's not my base for a troll trap. Just make sure the center area is big enough that the logs can't reach and you have room to dodge rocks.

For the crypts, bring a stagbreaker and smash it outside the closed door. Most of those bone piles are close enough to the door to get that way. Even if they're not close enough, you can get the skeletons cleared out and then run in and get the bone pile before too many more of them spawn. I always like to have at least ten points of armor before going into a crypt.