If he does a lot of thinking to himself, have you considered changing the novel to first person? Of your examples I quite like the 2nd, but if you're going to keep slipping into first person and italicising it, then why not write the whole thing in first?
I found your 1st example a bit awkward, and wouldn't personally recommend it.
If you were going to use the 3rd example, I think it should be 'He was assuming there was..' not 'He was assuming there's...' which I take as an abbreviation of 'He was assuming there is', and IMV would be wrong.
So:
He closed his eyes. He was assuming there was only one of them. |
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Or how about:
He closed his eyes, and realised he was assuming there was only one of them. |
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In another thread in this forum Terry is talking about invisible prose, and I think that's what you want to aim for, rather than variety. I think your (amended) 3rd suggestion is the most invisible, and you can probably use it again and again.
Deb
<Added>The second of my examples implies he's now wondering if he was wrong to assume there was only one of them, whereas the first of my examples doesn't give that impression - more that he is still assuming there is only one.