NGinx does work differently to Apache in that it does not .htaccess files (though this only slows Apache down). Though NGinx can be configure to work with CS-Cart SEO rewrite rules. I know not all users would know where to start, but with an auto configuration script it could be possible to setup the NGinx configuration for CS-Cart (currently all versions 2.xx and 3.xx). Simple guide to installing NGinx and running the configuration software would get 90% of users up running.
I think most users (this does not apply to shared hosting, unless shared hosting is already running NGinx) would prefer NGinx running CS-Cart. But most dot no where to start or find it all very daunting.
NGinx does look hopeful for CS-Cart, perhaps it may be a service you would look in to offering Adrian?
It is something I will look into, once NGinx is installed and running it is very easy to get CS-Cart running. Plus because it is not a memory hungry Apache dog it does result in improved stability.