Let me make sure I understand you correctly. You say you take your plugins and software with you to install on a client's (read stranger's) computer so that you can work your magic on their project.
If this is the case, I assume the first thing you install would be the latest eLicenser (or iLok if need be) software/drivers on your client's computer. Then you install Nuendo and the plugins. So far so good. What mystifies me is why would you prefer NOT to attach the dongle(s) before you start Nuendo. You say some plugins work (i.e. easily recognized) and some don't if their dongle is not attached. You of course know that every DAW out there scans the installed plugins while running for the first time after installation, and Nuendo is no exception. Nuendo begins to scan, and each plugin may "behave" differently according to their specific "nature" when meeting with Nuendo for the first time. So all is normal as far as I can see, unless I'm totally missing your point for some reason.
As for the key commands and prefs, although it would be very nice if we could save our preferences and key commands on the dongle, unfortunately it's not possible. A not so annoying work around would be to save the necessary files on a USB memory stick and replace them on your client's computer after you install Nuendo.
System 1 (master): Mac Pro 12-Core 2.93GHz, 16GB Ram OS X 10.8.5/10.10.2, Nuendo 6.5 64bit, Cubase Pro 8 64bit, M-Audio ProFire 610
System 2 (slave): Core i7 3930K, Intel DX79SR, 64GB RAM, Win7 64bit, M-Audio Projectmix I/O
MacKie HR824, Roland XV5080, 3x 24" LEDs, Multiple SSDs & 2-3TB HDDs, VSL VE Pro, MIR Pro, lots of toys