These are just anecdotes, but: I've used my pandora as a USB gamepad and my dev setup is running on-device off an external HDD connected via USB. Both pretty much require me to use it with a connected USB device. Also you have to take into consideration the power cable, which may well be connected while the device is in use.USB ports on the sides? Doesn't seem it'd be easy to hold with a cable or device attached like that, don't you think?
If I've got a USB cable plugged it then I'm sitting on the desktop - it's too unwieldy to use as a handheld with anything plugged in, I've found.
Anyway, these are just special cases, and if you do consider only using the builtin controls without any cables connected, then having the connectors on the sides is no issue. I'd still argue that designing ports on a handheld based only on use cases where it can not be held in hands sounds kinda weird