If one of them is bad, the charger will kill the other one too. If they are differently charged, it will kill one of the batteries and next time it will kill the other battery. (Kill as in make worse and worse until it finaly doesn't charge at all.)
I have mostly stopped using rechargeable AA and AAA batteries because of the bad quality of the last ones I bought. They took 3-5 charges before dying with a good charger that does all batteries separately.
Even the charger that Panasonic sold with the Eneloops requires matched pairs.
The other issue being that NiMH seems to top out at AA size. Finding C or D sized rechargeables is basically impossible.
https://www.amazon.com/Panasonic-K-KJ17M3A4BA-Individual-ene...
For a long while I kept them to prove the point to anyone who thought I'd must have lost my ability to distinguish plus from minus.
Edit: I have a Powerex MH-C980 and that has significantly made using NiMh easier. Before with a bundled Panasonic charger I had to charge everything in pairs, 4 max. The Powerex I can charge 8 cells individually, turbo charge if I'm in a rush, and see how much energy actually was used if something seems to be eating through a lot of batteries.