Train could slow a little with Clady's injury. Broncos are likely to add blocking help to Manning's blind side - which probably means more blocking from the TEs. If Dreessen is healthy, he'll get more blocking assignments. If not, Thomas will probably be asked to stay and block more frequently.
Broncos could run more two-TE sets, but that will come at the expense of Welker and/or Decker. It will also help defenses better key on the receiving threats. Either way, there could be a reduced number of routes for Thomas going forward.
Thomas is a pretty bad pass blocker at this point. I doubt Denver keeps him in to block too much. Honestly, he probably does Denver more good as an outlet receiver in a pass pattern than trying to slow an oncoming rusher.
2 TE sets come almost exclusively at the expense of Welker. Demaryius and Decker are outside receivers, they're on the field in almost all formations. Against New York, Welker was on the field for 49 snaps. Virgil Green, Denver's second TE, was on the field for 27 snaps. If you add Welker's snaps and Green's snaps together, you get 76 snaps, which just so happens to be the exact number of offensive plays Denver ran against the Giants. This is not a coincidence. Snaps are a zero sum game between the slot receiver and the second tight end.
Some more snap math: Eric Decker and Demaryius Thomas combined to miss 12 snaps. Andre Caldwell and Jacob Tamme each got 6 snaps. Again, everything lines up perfectly. 6 of the snaps Decker/Thomas missed came because Caldwell was on the field, which means one of the outside WRs probably needed a breather so Denver subbed in their backup outside WR. The other 6 snaps came with Denver's 3rd TE on the field, because Denver ran a half dozen 3TE sets in the 2nd half to get the running game jump-started. Knowshon Moreno + Montee Ball + Ronnie Hillman = 76 snaps. Again, everything works out perfectly because Denver is always in 1-back sets. Julius Thomas played all 76 snaps, because the in-line TE plays in all formations.
Denver runs such a wonderful offense because it's so predictable. Every single formation features an in-line TE (currently Julius), two outside receivers (currently Demaryius and Decker), and an RB (currently a committee, although Hillman only received 2 snaps against New York and seems to be on his way out). After that, Denver alternates between a third receiver (Welker) or a second TE (Green). Outside of some truly rare events (such as the half-dozen snaps Denver spent in a 3-TE set against New York), you can always tell ahead of time exactly how the snaps are going to break down.
That's why it's going to be so important to see what Denver does with Dreessen when he comes back. If Dreessen takes over as the 1st string in-line TE, Julius Thomas will fall from playing 100% of Denver's offensive snaps to playing about 33%. That's a pretty rough tumble.