Is it more memory/processor-efficient to open many windows in one desktop, or to make all these windows fullscreen? I have many, many windows that must be open all at once (VM, Email client, browser, IDE, source navigator, issue tracker, notebook, etc...), and have often bumped up against my MacBook's 16GB of RAM. Would it be more efficient to have these all in 1 or 2 desktops, or to have as many as possible fullscreen in their own desktop?

My logic here is that if they're all in 1 desktop (or 2 with a 2-monitor setup), then the Mac doesn't have to track which desktop each is on, and can use that memory for other things. On the other hand, if I have many fullscreen windows, then it doesn't have to worry about what may be in front of / behind those windows, because it will only be them and maybe a preferences dialog, so maybe it wouldn't care at all about windows on other desktops, or in other fullscreens.

Intuitively, I also feel there must be a performance hit from having so many virtual desktops open. I don't know how Mac OS handles it, but I feel like there's probably duplicate objects there (perhaps each has its own menu bar, dock, icons, etc.)
To expand on patrix's point in comments above, essentially OS X keeps track of every open window regardless of where it is, because there is a process(es) running each window. It also manages RAM usage, taking from the poor (less recently used open programs) and giving to the rich (program currently being used). Even if a program has an open window on the same virtual desktop, if needed, OS X will cull RAM from that program to feed the currently active program.

It's theoretically possible you would incur a graphics performance penalty for having everything on one desktop, especially if you have transparency enabled, but otherwise, there aren't really any system implications. So, basically, do whatever works best for your workflow.