I like C, though I'd like to see some of B mixed in. For nonessential items - like your honey that adds 10% hp, etc - C is fine, if access to the item is lost, just build the unit without that bonus (although it'd be good to inform the player that the 10 dread knights he just queued up will lack that bonus).
For items that you don't want to simply leave out, like armor and weapon, I'd prefer B; to see the unit still get built without the resource, just slower. If your unit uses an iron sword, and losing access to iron means you either have to redesign a new unit with a bronze sword (A) or choose a replacement sword when you try to build the unit (C), either way it's painful micromanagement. And not just micromanagement when you're training the unit, but it creates more micromanagement later - units with iron swords may perform noticeably better in combat than otherwise identical units with bronze swords, so you now have to keep track of which units in your army use iron and which got the bronze, perhaps relegating the bronze sword units to city garrison or acting as a rear guard over your supply lines, while the iron sword units are the front line, first to attack. This may sound fun and tactical, but multiply it over potentially hundreds of units, and it'll just be a pain - for simplicity's sake I'd much rather know that every unit of a given type has an iron sword, even if it takes longer to build them without access to iron.
A good number, I think, is 2x build time without the resource; i.e. if my soldier with an iron weapon and iron mail normally takes 15 turns to train, he should take something like 30 turns to train without access to iron. Of couse it's more complicated than that, what if he uses an iron sword but leather armor and you lose access to iron? However the details work out, though, I think it should wind up taking about twice as long at the most without a resource. This is a big difference, it makes you want to get access to iron, but not such a massive difference that it's no longer worth building the unit if you lose access to the resource. Keep in mind that, if you temporarily lose access to iron and you need units asap, you always have the option to build an older bronze design - but unless I'm desperate, personally I'll stick with building the iron design half as fast and focus on getting that resource back.
Option C, but keep the "bonus equipment" as part of the unit, just greyed out on the units profile. If/when your empire re-aquires the resource, you can move your unit back to a city, and hit "re-supply" or something to bring that unit up to standard.
This is a great idea too, it lets you get all your units back up to standard later if you temporarily lost access to a resource, so you don't have to worry about some units of the same type having different stats (which I'd really like to avoid having to micromanage).