For example, can you only access it using Wifi, or can you open a Linino terminal over a USB connection?
You can open a connection via LAN or or WIFI
I am a Windows user, so I use Putty to connect but there are similar programs for Unix.
When you have made the connection you will feel at home since you are used to Unix.
The preferred language seems to be Python and PHP, and for databases SQLite or MySQL.
The Yun has an SDcard slot, can that be used as a "hard disk" to store Linux software?
Yes and it is recommended to do so, as the flash ram has limited write cycles.
I haven't bought a Raspberry PI because I don't have a TV and, in any case, I already have a Linux computer. The Yun looks like it might be a better package of Linux and I/O. But if the Linux side is very limited I will continue to work just with my Uno or Mega.
I use the same technique with my Raspberry Pi.
The difference is that on the RPI you have acses to the GPIO from Unix, on the Yon you can only access the GPIO from the onboard Arduino Leonardo. (They are conected threough the Serial)
The connection between the two sides is through the Bridge Library