They are 'alive' when they are upgrading if you are comparing them to defensive buildings. If your AQ is upgrading to level 10 she will still be there on your base as a level 9 to defend it during clan wars.
I'm not trying to be rude but you aren't the first to suggest this as a recourse to using heroes offensively during clan wars.
This halfway house has been suggested multiple times and I for one think it is a good idea but SC haven't said anything more recently than there is a technical issue around it and that it is not ruled out to happen eventually.

