Are chicken bits left in space-qualified ICs?
The definition of chicken bit in Wiktionary is incorrect, and the extension by OP [as hardwired] is even more wrong. 

The chicken bit is a configuration bit (software configurable! and usually undocumented) that is incorporated into a design to disable a WORKAROUND of some issue discovered during bring-up of early silicon stepping. The bit is usually incorporated because the pre-silicon validation/verification of the workaround is usually incomplete at the moment of tape-out of a new chip stepping (typically due time-to-market constraint), and all consequences and possible side effects of the workaround are not known yet, as compared to much more verified initial design. The chicken bit is a way to undo the entire workaround in cases when some new side effects would be discovered in process of more thorough and complete post-silicon validation. 

As such, the chicken bit is no different from other configuration bits for other hardware features, and should not cause any special concern. In modern designs the essential configuration bits are protected by various special lock-unlock-sync mechanisms, so the run-time effect of SEE events on hardware configuration is minimized.