Probably not.
Maybe not allies exactly but it wouldn't surprise me if this incarnation of Bebop and Rocksteady helped the Turtles if only so they could get away from Shredder and possibly earn some retro-mutagen if Donnie can whip some up.
Until he decides to get rid of them for failing him too much.
Knowing this Shredder, he's nothing like the old Shredder who was all goofy and never killed his loyal henchmen. I don't know how things will play out if they were forced to stay with him.
Vgiannell5:
That is very true. If they are going to fail hime too many times he will get rid of them. The Shredder does not like failers.
...or will they!!
Dun dun dun!
Anyway, considering that it'll most likely be against their will so they stay alive, I guess I can see them plotting behind Shredder's back, but I highly doubt that they'll become allies with the turtles.
Probably not.