[afedchin]

1. Is a 3D-iso movie always real 3D (frame packed), or can an 3D-iso also be a SBS or HOU?

3D-iso contains 2 video streams. the first is monoscopic video stream (for backward compatibility with old BD players) and the second one is a special stream with coded difference between base and another view. "frame packed" it's a HDMI output mode. 
 

2. Same question as 1. but for mk3d

mkv (or mk3d) it's just a container. it can contain the same two streams as 3DBD or 1 vide stream combined from 2 streams (base + difference) or re-encoded to TAB or SBS video.
 

However if I take the projector-remote and switch off the 3D function it shows me a splitted HOU view.

It's because RPi video driver uses HOU (with 45 line space) output mode (see HDMI spec). there are a lot of possible ways to transmit stereoscopic video through HDMI and one of them called frame packed.