Barend’s got a great article here at the COW that covers interlacing with AE.
As for your Qs:
1)Either way is fine since you’re not rendering to fields. Stretching in the Output Module may create field mush IF you render out with fields.
2)Your footage, when interpreted correctly would have its fields merged to create a frame in AE. So effectively, you are rendering out from AE, not the original interlaced footage. And AE will be looking at the frames. You don’t lose any pixel resolution but you will lose some motion smoothness going from 29.97 interlaced to 29.97 progressive.
3)Asking any computer to playback 59.94fps in realtime may be a bit too much to ask for. The fact that it is destined for the Web only compounds the issue. There’s always a compromise between quality and efficiency when delivering movies for the Web.
In fact, you may want to look at a lower frame rate than 29.97 for your Web movie. Try 18fps. That will lower the bandwidth requirements; making your movie more accesible to viewers.
HTH
Roland Kahlenberg
broadcastGEMs
customizable animated backdrops with Adoeb After Effects project files