I've been putting some thought into this because it seems like really big thing for GW not to notice and I've come to a conclusion:
The Mawloc's Terror from the Deep attack can't hit zooming flyers.
This actually has nothing to do with the "blast marker" being a "blast template" but instead with a couple of rules and a bit from the Tyranid FAQ.
Firstly, what kind of attack is the Mawloc's TFtD? It's a shooting attack? Why? Well let me quote the FAQ first as it's essential to my point of view on this:
Q: Can I take cover saves from the Mawloc's Terror From the Deep attack? (pg. 51)
As many may recall, cover saves can only be taken against shooting attacks, not close combat attacks. So since it's a shooting attack we take a look in the main rulebook at the rules for shooting at a flyer:
Hard to Hit
Zooming Flyers are incredibly difficult targets for troops without suitably calibrated weapons and scopes. Shots resolved at a Zooming Flyer can only be resolved as Snap Shots (unles the model or weapon has the Skyfire special rule as described on page 42). Template, Blast and Large Blast weapons cannot hit Flyers in Zoom mode.
-Page 81 of the 6th Edition Rulebook
Did you catch that? Shooting attacks that are made by models or with weapons without the Skyfire rule are resolves as Snap Shots. And since the Mawloc doesn't have the Skyfire rule we move onto Snap Shots (don't worry, I'm only going to quote the part related to this whole thing):
It's important to note that any shooting attack that does not use a Ballistic Skill - such as the Necron Monolith's portal of exile - cannot be 'fired' as a Snap Shot.
-Except from "Snap Shots", Page 13 of the 6th Edtion Rulebook
So, as the Mawloc does not roll to hit against models that are touching the Large Blast Marker for the Terror From the Deep attack, the Mawloc can not hit Zooming Flyers.
At least this is my understanding of the rules.