So I've been at the Hound Pits at the start of the game for several hours, exploring every under rock, water, bush, every room and everything i could, but there are still some inaccessible areas like some locked doors and a weird hatch in the ground not that you can somehow interact with. Do these become accessible later? I can't really find anything else collectible at this time, so should I move on now to the first actual mission?

Sewers become accessible later.... and there's an abandoned apartment that Cecelia has a key to and will give to you later, if your Chaos score is low.

Hound Pits also become available later, as part of the main quest.

Patience, young Padawan all in due time.

One more question. The big tower, there seems to be an open window closer to the top and you can look up through the floor of the towers second floor and it almost looks like a place you could go to? i mean besides that one small part of the tower you can go into.

Big tower is accessible though a window by where Corvo's bed is.

Oh yeah I know that, I went to the part of the inside tower you can go into, but can you go up higher later? Like i said, closer to the top of the tower there is an open window, and in the room you can go into, looking up through the ceiling almost looks like an accessible area.

You can only go "higher" in the tower when in the void. And while you are there you will see why you can't go there in the real world.

Hmmm.... I'll have to check on that next time I'm at base. Anyone else know?

EDIT: Ah, thanks Sour