I'm beginning to think that YA books set in Venice is another trend (yes, I'm seeing trends everywhere -- blame BayCon and the "Beyond Harry Potter" panel they've scheduled me for -- and it will probably only get worse as we head toward the end of the month).
Venice certainly has to be one of the most inherently magical cities in the world -- although I was less impressed than you were, GrownUp, with the two books you mention, my favorite alternate-world Venice being Tanith Lee's definitely-not-for-children version in the "Secret Books of Venus."
But now I've found another recent YA book with a fabulous Venetian setting. Just picked it up yesterday (after trips to two local libraries already this week, the message that this particular book was in convinced me that another library run was quite in order) and read it before bedtime, it sounded that entrancing.
The Water Mirror by Kai Meyer, translated from the German (the original title was Die Fliebende Koenigin, which I take to be The Flowing Queen, but Gollum or someone else who actually speaks the language may correct me) -- an alternate-history fantasy in which shark-toothed mermaids swim in the canals, guardsmen patrol the city mounted on animated stone lions, and much of the world is under seige by the armies of a resurrected Egyptian Pharoah.
The prose style is, unfortunately, somewhat lifeless, and the characterization on the thin side even for a YA title (both of these may be faults in the translation) yet I was charmed by the setting and by some of the ideas, and I'm not surprised that the book was a hit in Germany and has been translated into fourteen languages.