There will be a 25% reduction in capacitance, which is already suffering from series string disease. I don't know that it really hurts them if they occasionally nudge a little over 2.5 volts. The weak link is the dielectric layer, which in this case is very thin. Excessive voltage will cause a breakdown, which may or may not be self-healing. One day if/when I have a spare one that I don't need, I will run some tests. It certainly would be useful to know what is the failure mode of these things.
Connecting a series string of zeners directly across the capacitor/battery is a bad idea. A transient spike, perhaps from the starter motor, could zap one or more of them, resulting in disaster. The proper way to do it is to have a transistor across each capacitor, turned on when the zener starts conducting. Probably cheaper and safer to just buy a balancing board. The LED idea is appealing because of its simplicity, but it doesn't really do the job, and can't dissipate enough power to drain away the excess charge quickly enough.
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