Taking into account security (as opposed to safety) in aircraft design will IMO have huge consequences.
The big issue is that redundancy by identical systems is a standard safety protection. Not perfect, but works. E.g. having two identical GNSS units, two identical radios, etc. If one breaks down, the other one still has a good chance of working.
But redundancy by identical systems is worthless for security protection. If the attacker can disrupt one, it can disrupt the second identical (or similar design) one. E.g. on an ILS, someone in a van sending a jamming signal on the ILS frequency, or a stronger signal giving false information.