I don't have a source, but it has been mentioned several times that the effects were done at 720p, since that's all that could be broadcast.
720p would make sense as an output format for the entire episode for broadcast, since the majority of TV stations, even now, are broadcasting HD in 720p, and for those broadcasting in 1080i, an up convert wouldn't be as noticeable, because of the amount of compression that will be put on the signal by the time it reaches your house it will not be anywhere near what was sent out, and by the time it does reach your house, it is closer to the next lower resolution on Blu-Ray/ DVD; but for future use it would make sense for the effects to have been done in 1080p. It's just like streaming and downloading video over the Internet where the signal needs to be compressed to be more manageable. If you look at "Smallville", where the Season 1 effects were done in 480p, it is possible to make HD 720 videos for those episodes available because the compression put on the video and file will negate any problems caused by up converting, and still make them look as good as an up converted DVD.
For TV broadcast, even if the video is sent out at 720p, by the time it reaches your house, the signal will look no better than a 480p upressed DVD. A 1080i signal will look no better than a 720p signal on Blu-Ray. Same goes for Internet video. And 1080p currently is not offered because, with the amount of compression needed to transmit a 1080p signal with current ATSC and other digital standards, would result in an image that looked like it came from a VHS tape recorded on SLP.
So when Enterprise is released we will be seeing the HD versions in a much better way than we have seen it on broadcast, or in Internet streaming/download. It still won't be the full quality of the original masters, but it will be better than the current versions that are out.