Can writing in the third-person limited omniscient POV include internal monologue and character thoughts?
Depends on what your "limit" is.
If you are limiting yourself to one character, then yes: the Harry Potter series is told in third person limited omniscient, and we get Harry's thoughts, but no one else's (other than two or three specific chapters in the entire series). But if something doesn't happen to Harry, or if he doesn't see it or hear about it, then the reader can't know it.
If by "limited" you mean that you are telling the story as though you are describing a movie, so the reader can see actions going on at any place or time and focused on any character, but can only observe the action through the five senses, then no: you aren't giving anyone's POV.
Pick one and stick with it.
Constant switching between third-person and character thoughts is definitely considered bad style (advice taken from here: http://www.amazon.com/Write-Novel-Them-Misstep-Misstep/dp/0061357952, funny and useful book btw)
However, if you are telling someone's story throughout the novel - then is acceptable if you would also write down the protagonist's thoughts.
If you write several character thoughts constantly the reader might start feeling like he's going mental :)