Emacs does not currently try to handle case 3, as far as I know. That would be a medium-sized project in its own right.
Case 2 depends on per-programming-language syntax tables, not on the spellchecker. I don't know what the current arrangements for this are.
Case 1, on which everything else depends, is a matter of Emacs sending stretches of text to the spell-checker, which currently (at least with Hunspell) does not deal with punctuation very well, though there are plans to improve Hunspell, according to the issue I linked to earlier.
None of these would benefit from special-casing treatment of the period or any other character in ispell.el, I think.