The bad news is no, subfloor products won’t make up for an uneven floor. The good news is that I don’t think concrete sticking to the plywood will be a problem. There are two reasons why:

1. First, it’s traditional practice to install a layer of tar paper over a wooden floor before pouring a mortar bed as a base for tiles. This means that when you break up the mortar it’ll probably come out nicely in chunks.
2. Second, even if the installer did pour the mortar right on top of the wooden floor before installing tiles (highly unlikely), ordinary mortar doesn’t stick to wood very well. A square-mouthed shovel should clean it off nicely. This works well for all kinds of subfloor preparation, especially if you take the time to sharpen the tip of the shovel beforehand. A file or bench grinder does a great job.