So here are my questions:
Are nuclear weapons available and in what version of HP are they?
Yes nuclear weapons are available. They are available in all versions of the game . Both games give you the ability to turn their use on and off depending on your wargaming preference.
Does the AI simulate it on a realistic basis...responses to responses and so fourth?
Harpoon Classic had a response trigger where as in Harpoon 3 it depends if the scenario was designed that way. As mentioned above you can just turn the option on in either game but most scenarios are not geared to be nuclear exchanges. You can create your own in the scenario editors however
Are their land based ICBM's, IRBM's, MRBM's and so on?
Yes, the databases for the games are quite extensive. You will find all the nuclear weapons your heart desires in many varieties
Is the nuclear option readily available in most scenarios?
It depends on the design intent of the scenario. You can turn your nuclear option at any point but it would depend if the scenario was designed with a nuclear weapon in it.
To be perfectly clear Harpoon is focused on Naval and air warfare. The nuclear weapons are included but are not the focus of the game. So if you want to be a mushroom cloud laying mammerjammer you certainly can be. Just realize that you may have to design your own scenario with the scenario editors or search for scenarios where that is the focus.
What is the best version for this type of simulation?
Difficult question as everybody has an opinion and has been historically a heated debate within the community. My personal preference is Harpoon 3 although I enjoy Harpoon Classic as well. I would suggest just downloading the demo's of each and checking them out. Much easier way in determining your preference.