ORAC,
As I might not have made clear, the Harrier layout, (with two of four nozzles cold and all four shielded to an extent) helped reduce IR susceptibility against early generation threats. Sorry for any confusion.
However, the location of the nozzles mid way along the fuselage always meant that a hit would be more serious than on an aft engined design.
Again, there is complexity, depending on the warhead size, angle of arrival and lots of other classified stuff that (thankfully) I am not up to speed with.
As missiles got more capable, the equation changed. That's again quite a normal state of affairs for this area of aircraft systems design.
I am familiar with the TERMA pod effort on GR7 and Tornado for the 'Stan, and would certainly agree with the Navy's assessment that it is less costly to design survivability into an aircraft than to try to add it on later. That, of course, is where the design of aircraft like the F-35 has headed, where just as much effort has gone into addressing IR signature as in the RF area.
There is absolutely no doubt that two engines offer key advantages in the area of survivability. Unfortunately, as I've pointed out, they also tend to lead to very large aircraft that are unaffordable. Nobody, as far as I know, starts out to design a twin engined aircraft that needs only one engine to achieve its required performance. (As ever, development of aircraft and engines go hand in hand - sometimes the engines lead, sometimes the aircraft)
Hornet may be an exception to the 'two engines too big' rule because: a) it started out as a light weight fighter design (YF-17) and b) the demands of carrier operations acted as a natural brake on weight growth.
Best regards as ever those doing the business,
Engines