I'm making a mocha hot fudge sauce with , among other ingredients: corn syrup, bittersweet chocolate, cocoa, coffee and possibly rum. Should I use regular or dutched cocoa? The recipe doesn't specify.
It won't make much difference here. Natural cocoa is usually a richer, darker flavor, though dutched is visibly a darker color. With the bittersweet and coffee in the mix, you probably aren't lacking flavor or color, so it's up to you!
If you just want someone else to decide for you: I say use "natural" because I like the flavor.
what about the acid/alkali issue? Or is it a non-issue in this application?
I'd say the acid/alkali issue doesn't matter. I would just go with my favourite cocoa powder if in doubt. My favourites are Cocoa Camino and Green&Blacks.