Which would have better handling potential, '95 Civic 2-door thing, or a 96 hatchback? This is with upgraded shocks struts coilovers and what-not.

Hatchback - stronger structure, better weight distribution.

probably the same but if i had to say one i would say the 3 door

It really depends. The Hatchback would be quicker since it has a shorter wheelbase, but the coupe is more stable because of the longer wheel base. Both would have the same rigidity.