The word suboptimal is not always considered a word in itself (that is, it is not given its own definition page), but it is understood. Dictionary.com gives the definition which you guessed at, that is:
being below an optimal level or standard.
In the contexts I have heard, the word usually uses its literal meaning. It does normally indicate that something is lower than optimal, enough to be noticeable. However, it does not have to be a gross overstatement--especially not in academic works.
The authoritative Oxford English Dictionary includes suboptimal on its page about the prefix "sub", noting that it has been used since 1901 in academic journals:
1901 Amer. Jrnl. Physiol. 4 477 If the stimulation is *sub-optimal, the animal will seek the source of light.
1980 Sci. Amer. Sept. 134/1 On the whole, however, India remains a case of stunted, suboptimal growth, burdened as it is with the world's largest single national mass of poverty and unemployment.
Because of where this phrase has been used, I would say it is perfectly fine for usage in an academic or semi-academic paper. You can write it "sub-optimal" to emphasize that "sub-" is the prefix, or "suboptimal".
The prefix "sub" means "under, below". If I heard "sub-logical" I would assume that it meant something less than logical. It would be interpreted correctly, and you could technically coin any term with a prefix that you wanted. There are no "rules" for what you can pair "sub-" with, as far as I know.