Yeah, you can do that. How it can be minimized depends on what NSF you want to use. If you have source code it's no problem to relocate it, but if it's a ripped NSF fitting it into an NROM (with lots of other data) could be trouble.
I know of a program by TNSe called NSFTool that is great for optimizing NSFs, you could have that clear all unused bytes for one particular song playing for a given amount of time. I don't think it was ever released though, I lost my copy of it.
But there's no guarantee that the free space won't be spread throughout the file, so it still depends on the NSF.
I always optimized NSFs by cutting out parts of it with a hex editor, if it stopped working, revert to the previous backup, heheh.