The game is randomly generated, so yes, there will be times where you can't get certain items. I can't even begin to tell you how many times I've had to skip item rooms because the game just decided to be skimpy with the keys that run.
That said, there are often ways around certain problems. For those items on the other side of gaps, you can bomb a rock that's next to the gap. Most of the time, the blast will push the rock over onto the gap, making a bridge you can cross. There's also a ladder that lets you cross single-block gaps, and there are many items that let you fly, either permanently or just for the room you're in. The more you play, the more you'll start to learn the various ways you can get to things.
The rooms with the tooth doors are just rooms that hurt you when you go through the door. You're taking a risk with those that the reward in there will be worth the lost health. Sometimes a secret room will be next to one, then you can bomb your way in and out, but not always.
And yes, there aren't any visual cues as to which walls you can blow up, but there is a pattern to where the secret rooms are located in a level. It's not 100%, but once you learn it, you'll be able to improve your odds of finding them.
On the other hand, there's also items that make it trivial to find secret rooms. You'll eventually find an item that makes your shots explode, so you can just check every wall for free, and there's another item that straight-up just shows you where they are.