IMO, the advancement info for the owl in the MM is in error. It ought to be 1 HD (Small); 2 HD (Medium). A great horned owl isn't as large as a good-sized golden eagle, but they'd both be medium-sized in the D&D categories. I don't see how you could call anything with a wingspan of less than 7-8 feet size large, and there aren't any owls that get anywhere near that size IRL. That, plus the fact that size small is skipped in the advancement listed in the book, leads me to believe that it's an error.
A great horned owl (medium-size, 2 HD) makes a decent starting companion for a druid IME. Fun, not overpowered-I doubt you'll have a tremendous problem convincing a DM to allow it. Doesn't fit the 3.5 rules, of course, but that doesn't mean it couldn't get rule-zeroed in ...