If your FTP client allows for it, you can specify a directory to open. In example, in MidnightCommander while I browse the internal memory and the . directories inside home are hidden, I can simply:
cd ./.apricotsto access /home/.apricots
As for the file extensions, It's solely a matter of the MIME types inside the OPKs .desktop file. No matter what the emulator might actually support, if the person responsible for preparing the opk forgot to list one of the compatible extensions inside .desktop, it will not be displayed by gmenu2x's file browser.