I had the impression that having a ton of files in a folder vs a single zipped file would affect the fps, maybe I'm lucky since I have a SSD, it doesn't affect me that much, but I wouldn't be surprised if it was very different for people that have a regular hard drive, the game constantly having to load and unload different files from a folder vs multiple files in a .zip archive could be stressful for a regular hard disk...
It could be stressful if those textures were like 2048x2048 or higher and HDD was 5400RPM with crappy read/writes.
I'm actually running my MC from HDD [7200RPM Seagate Barracuda, fairly powerful little beast]. Tried to run it from my system SSD [Samsung 840 Series] and there was no difference in FPS [tested on loose files and archive].
CPU: FX8350 8 Core @4,5GHz Black Edition [shame that Java is badly handling mutliple cores]
RAM: 16GB Corsair Vengeance 1600MHz
System SSD: Samsung 840 Series [128GB]
Data HDD: Seagate Barracuda 7200.12 [1TB]
GPU: EVGA GF GTX770 SC ACX 2GB
If you experience drops, consider locking your framerate using nVidia inspector. I'm running my MC with constant 60 FPS. I was having like 300+ before, but no kiddin', there's no difference between 60 and 60+, at least for me.