I think I found the solution. There were a couple of roms without "[!]" in the name. Because I was trying anything I could think of, I deleted those files and now everything is fine. Emulation shows every N64 rom now.
Sorry for asking your help. Thank you for thinking with me for finding a solution.
Currently RetroPie automatically copies files (roms and configs) from a USB stick to the Pi. Is it possible to disable this process so that it happens on command rather than automatically?
Yes, disable the usbmount service and the synchronization will not happen automatically.
Also is it possible to reverse the process so that the USB stick can be used to mirror the contents of the Pi, or at least select folders from it, either automatically or ideally on command?
Yes, it's possible, but there's no provision in the RetroPie scripts for this kind of scenario.
When you want to keep your ROMs on an external drive, you create a retropie-mount folder on it and RetroPie would sync the ROMs from the SDCard to the disc, then it will mount the disc so you can use it.
If dont' want to use the external disc for the ROMs, but just synch to it, then you'll have to create a script to do it. Both synchronization methods (USB to card and vice-versa) use the rsync command, you can easily create 2 scripts to do this synchronization and add them under the retropiemenu system so you can call them directly from Emulationstation.
My guess is that the best way to do this is to install Linux (e.g. Ubuntu 16.04) to a USB drive and make it bootable.
Then boot into Linux from that USB stick, and install Retropie following the instructions on the RetroPie website for x86/64 Ubuntu.
When you want to enter the world of RetroPie, simply boot the USB stick from the computer UEFI/BIOS boot menu.
I imagine that you'll want to use a fairly large USB stick to hold all the ROMs you wish to use.
64GB or even 128GB would almost certainly get you the bulk of the decent emulators.
@seeker But, sorry, a noob question. I plug the USB with the roms (zipped), anyone in its folders, and when I turn on the Raspi, all the roms will be transferred to Retropie, isn't it? Well, I have to wait the yellow light stops blink. But, I waited near six hours :S and it continues blinking. I turnoff the raspberry. Is it normal? I'm really sorry to ask something so simple, but... I suppose I'm very clumsy. And I was looking for an answer, but nothing.