The thing is, Gendo and SEELE don't consider the mental states of their pilots to be important. They certainly didn't care at the high point of canon, and there is no evidence that there was any change in their behaviour when the pilots started to suffer mental breakdowns. It was completely irrelevant to them all of this time. Trivial, petty details. SEELE has no time to pay attention to such little things when they're planning to end the world and become gods.
I mean, sure, the audience knows that their mental state is vitally important, but that's leading to a bit of bias here. The Children are the main characters of the show, but in-universe no one would know that. To the secret masters of world, they're just expendable pawns to further things along - and there's also the fact that they're just a bunch of teenagers; "They're not important in the overall scheme of things", "what can a bunch of children do against us anyway", "They can be replaced if they break".
They did have the replacement candidates and the dummy system as backups. Oh, and remember the complete lack of fucks Gendo gave when he activated the dummy system and Shinji went on his tantrum?
Even with Rei, who was pivotal to Gendo's plans, Gendo never really cared about her. In canon, though Rei died and should have lost a good deal of her memories, and despite the fact that she should have been indoctrinated for most of her existence to let Gendo use her to end the world when the time came, she ended up giving control of Instrumentality to Shinji instead. She was literally neglected enough to rebel against the entire point of her existence (partially, because she still triggered Instrumentality)