My Longbowmen can upgrade to Mechanized Infantry *shrugs*
Upgrades aren't a matter of realism, it's game balance. Same reason why Missile "cruisers" can't defend against air attacks. It seems perfectly logical for Stealth Destroyers to simply be Destroyers that are also invisible. Why invest the hammers or upgrade-gold if the unit isn't clearly better?
I do think that upgrades are a convinent thing so the AI doesn't running around with spearmen in the modern times as it often did in the civ games. But an AI running around with destroyers instead of Stealth destroyers is no problem with me.
To upgrade a longbowman to a rifleman, simply exchange his bow for a rifle, and then make that rifle automatic and yes an Infantry. If you then give him something to drive - Mech Infantry.
Personally I don't like Frigates - Destroyers upgrade either, but hey dress your old frigates with steel plates and exchange the guns for more modern guns, okey some (faintly) logic here. But to remove the hull and all external weaponry add Stealth technology hull and internal weaponry instead (yes stealth ships doesn't have missile batteries on the deck, it's inside the ship). It seams that it would be more effient to build a new ship.
It should be a standard destroyer and an Improved destroyer, like Spruence class destroyers and then improved Spruence class destroyers (none are stealthy, but the latter has improved radar and improved weaponry I believe. Or if you like it a Pre-WWII destroyer and a Post WWII destroyer.
But as I said above, a stealth ship can be configurated to act like any type of ship (missile strike ship, anti-submarine ship, anti-air ship). There was a mod (I don't remember which, FFH, I think) when you got a choice when you left port on what to focus on men, cargo, etc. The same could be done here, when you leave port with a stealth ship, what will it act like.