- Are mutants really performing better? In what way?
The draws in TE match up teams with about same quality.
But if you see those two players who have near quality, Van Nistelroy (with some mutant attacking skills) has an advantage vs Fernandez who has normal defending skills.

Click image for larger version.  Name: vn fernandez.jpg  Views: 222  Size: 82.8 KB  ID: 111716

Also players with some top skills, like 340%, "driving crazy" the game engine.
it's not only that an attacker has some high skills, at old times a player with 1500% fitness and strength, was performing like a superman.
The game calculations have broken with this system of training and advancing skills without limits.

In what way not?
Many managers don't have original mutants (players with 300%-1%).
Maybe they have 200%-10%.
In some cases the program ignores the quality/skills of players and counts in a bigger factor other things, like formation/tactics or presence of manager/win bonus/training bonus.

- If you bring them up to 100%, do they loose much training ability? Is a 99% fast trainer you bought to 100% much faster in training?
decreasing gradually

about mutants, my suggestion is to wait and see how things come as in one month we should know about the new TE2019 and maybe some things (like training) will change.