First of all, WB has plenty of HD. You're right that UPN has little. Since CBS is a HD leader (too bad I watch NOTHING on CBS), I would guess that CW will carry a majority of their programming in HD. Also, it appears that in most cities, the WB affiliate will be switching CW, and in most cases the WB affiliates are better equipped- many UPN affiliates don't even have HD capability. WB fought their way up to where Fox was 5 or 6 years ago, but UPN never really got out of the starting block.
If you look at the channel spacing on the current HD-LILs, there are 6 channels allocated for each city. They channels were mapped right before the CW plans were made public. My guess is the eventual plans are to add CW and PBS.