It hasn't affected me. I rarely use the 1/1000 speed on my MX, as it's actually more like 1/800. I've shot plenty of 35mm cameras (old Spotmatics and Russian M42 cameras) with a 1/500 top speed, and it never really limited me. With my MF system, I find I'm usually 1-1.5 stops more closed down vs. 35mm for similar situations. I think I've only used the top 1/500 on my ETRS 5 or 6 times so far-- I'm usually hovering right around 125 or 250.
The fastest film I currently shoot, though, is FP4+, so YMMV.