MGS3 HD
does play in slow motion when the framerate drops. That's an unarguable fact. Groznyj Grad's outdoor areas, Volgin's electricity and the flowers in Rokovoj Bereg all cause slowdown; not just framerate drops, actual slowdown. The final bossfight is particularly bad for this.
I imagine it's due to the game's internal logic being tied to the framerate in the original version, or something like that, which Bluepoint wasn't able to get past. Their Metal Gear HD Collection is like 99% perfect, with a few unfortunate niggling problems (Codec calls lagging, slowdown in 3, missing Snake's Nightmare, that kind of thing). The Dual Shock 3's face buttons are much 'clickier' than the Dual Shock 2's were, which makes the pressure-sensitive shooting controls a real pain in the HD Collection, though you can always just unequip your gun to put it away without firing (how did they get around that on the 360 version, out of interest?).
Despite all that, they're still by far the best way of playing the games, though. You could make an argument for the PS2 version of MGS2, since that game still looks amazing and that gorgeous sloshy rain on the Tanker doesn't quite translate to 720p, but MGS3 benefits so much from the higher framerate (and with Peace Walker they actually
tripled the original framerate

). I just hope the Collection makes its way to PC one of these days, because I'm sure you could cure that slowdown with brute force.