I can't say about the 8088, but I do know two things from experience: flight avionics are often upgraded, in commercial aircrafts; I wouldn't expect anything less with the shuttle.
The US military started a COTS program a few years back, to cut costs. The idea is to attempt to accept Commercial Off-The-Shelf electronic components, instead of paying an exorbitant amount of money for a part specifically engineered for a single purpose.
The program is doing well, but still has some issues, specifically with reliability, or more specifically, the life cycle of the part: they meet all specs, but fail within a relatively short period of time (i.e. 3 years or more).
Designing a new shuttle would be prohibitively expensive, indeed, but there are many preliminary designs that were shelved, and some others explored, during the past 25 years.
The most significant of these is a pseudo-commercial stratospheric airliner type of vehicule (dubbed X-30?).
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