I doubt that it would be a major problem. Obviously it's possible, but unless the engine is going to be consistently operated at high rpm I don't think I'd spend too much time worrying about it. I run a HV water pump on my 340 and the March pulleys on it have a ratio of ~1.04:1, so, that's almost 10% higher than the factory ratio for an HV pump. I haven't had any issues with cooling on my car at all, and it's a 9.8:1, .060" over, 340 with iron heads and 3.55 gears that I frequently run up and down the freeway at a constant 3,500 rpm. Granted 10% overdriven isn't 35% like it would be with the factory small block pulleys.
Looking at the factory numbers and ratio's, and working off of the advertised gains for a HV pump (20-30%) it looks to me like what they were doing was keeping the volume of water moved by the pump close to the same for the two systems. Which probably means they had done the cooling calculations based on that volume of water being moved, and just held that as a constant. The AC cars suffer from the radiator air flow being obstructed by the condenser being mounted out front, so they had larger radiators and overdriven fans to increase surface area and air flow to compensate.
Now you could argue that they optimized the volume of water being moved for the whole system, which is why they wanted to keep it close to the same. So, running the HV pump with an overdriven pulley might not be as efficient. But of course that assumes you have a factory radiator that has the same resistance to flow as what was originally calculated. Aftermarket radiators with different tube sizes wouldn't be the same either.
There's a ton of stuff to consider. I wouldn't worry about it, but if I was having problems with cooling it is something to consider.