PSTV (PS Vita TV, in Asia) shares the same exact OS with PlayStation Vita.
The only difference between the consoles is that Vita TV has a white list for "TV allowed Vita games". In fact, many Vita games have been "enhanced" to work with PSTV.
There was a hack for VTV to play not allowed games for PS Vita, but the flaw allowing it has been patched through software update.
So, the answer to your question is:
The PS TV (or Vita TV) is basically a screen-less Vita. It is detected by the server as a PlayStation Vita, and that's why you see two Vitas.
You are allowed to have two devices between Vitas/PSTVs, so there is no point to deactivating one.
If for some reason you NEED to deactivate one of them, the best way to do it IS NOT from the Account web page, but from the console itself:
Access the HomeScreen open the "Settings" app and browse into PlayStation Network settings. The menu will be pretty much self-explanatory.
With this method, theoretically you could do it as frequently as you wish (be careful just not to do it too often, unless you wish Sony to suspect fraudulent activity and close your account).
Note: Remember that you can only deactivate ALL of your devices from the web once every six months, and that kind of deactivation is only meant for people losing or damaging their console. It doesn't involve console doing anything, until it connects to the internet, of course.