I also have Win7 64-bit with 6 gigs of RAM, I'm running the New Interiors mod (plus a bunch of others). The framerate for me seems fine, no real change from when I was running without the mod in XP 32-bit.
Have you run the 4GB patch for SH3? The SH3.exe file needs to be patched to make use of more than 2 gigs of RAM - if it's not patched, it won't use the extra RAM you've got with a 64-bit OS no matter how much you cram in there.
The 4GB patch can be downloaded from the link in this thread:
http://www.subsim.com/radioroom/showthread.php?t=177274
Regarding JSGME (the mod enabler) - make sure your mods are copied into the game's MODS folder in the correct format.
When you download a mod and extract all its files, if the mod was "JSGME ready" what you should have is a folder named for the mod and inside that another folder named "data" in which are all the mods files (excluding any readme files and other documentation that the modder included, which are usually outside the data folder).
The whole extracted folder needs to go in the MODS directory in your SH3 game folder.
So the path to the data folder for the mod should be, for instance, "Silent Hunter III\MODS\[Name Of Mod]\data" otherwise JSGME cannot enable the files in the data folder because they will not be where they should be when it looks for them.