Steve,
Many variables in this.... It all depends on personal preferences.
Sunroof: Pro's: Open & close at will, esp if the weather turns. Unlike some of these MKIII & MKIV Targa owners. Nice to have sun/extra breeze coming in, on nice day. Sunroof retains most structural rigidity, versus those w/ Targa's (run a search on the targa "wet noodle" body rigidity). Hot days when you first get in the car... Open the roof, roll down the windows, turn on the fan. Hot air rises & most of it ends up going out of the roof. Helps in getting the interior cooled down faster. Cons: When motor starts to missbehave, problems happen (they've been well documented here). Outer sunroof panels have been another source for rust (another well documented item). Sunroof & the rest of the operating components add's weight (not too much of a big deal, unless you're trying to put the car on a weight diet for racing purposes). Cut's down on head room (for really tall peeps). System becomes a water leakage nightmare if the drain tubes are clogged w/ crap.
Hardtop (no sunroof): Pro's: More structure rigidity than Sunroof cars. WAY WAY more than Targa cars. Extra headroom for peeps that are tall. Less overall weight (good for those who want lightweight for racing purposes). No issues w/ overhead water leaks. What else am I missing?? Cons: No overhead open air/sun coming in from the top. Takes longer for interior to cool down (even w/ windows open & fan on full blast. My 80 MKI Brownpra was a Hardtop). No extra overhead maplight, that you would get w/ the Sunroof control switch. "Finding" a intact Hardtop car, that has not had a aftermarket sunroof installed (for those trying to specifically find a Hardtop). What else did I leave out??
Again, it all boils down to personal preferences. If you are purposely looking for a hardtop, I would look around for one specifically, rather than trying to convert a sunroof car into a hardtop.