This is admittedly a partial answer; it was originally inspired by GandalfDDI's link of JSC-48029 in their answer. That document notably calls out whether or not selected airfields have PAPI lighting, "BALL BAR" lighting, and MLS (not ILS! see further on). Many have none of the above.
JSC-23266 - Approach, Landing and Rollout Flight Procedures Handbook - Rev B 2005 05 (also on GandalfDDI's site! thanks!) doesn't seem to consider the PAPI-less case, and takes it as a given that the PAPI lights are adjusted for the 20-degree Outer Glide Slope. See e.g. section 188.8.131.52 "On the OGS", where
If MLS data is incorporated, navigation, and therefore guidance, is very accurate. The HUD guidance diamond is the primary flight reference with the PAPI lights as a cross check. The PAPI's are true information but with MLS,
the guidance diamond (or needles) provides a simple method of smoothly tracking the OGS and the extended runway centerline. ... Of course, there are two red and two white PAPI's for a 20° glide slope, or three red and one white PAPI for an 18° glide slope.
When MLS data is not available or not incorporated, navigation and guidance information is only as accurate as the TACAN system. This level of accuracy is adequate for flight around the HAC, but is generally not sufficient to precisely track the OGS. Therefore, the PAPI's are used as the primary glideslope reference and the overall visual scene is used to determine lineup errors.
Of some additional interest in this document are appendice tables A-I and A-II. A-I is a list of "Space Shuttle Approved Landing Sites" (with a redirect to the document that will be the most current list); A-II is a much shorter list, flight-specific example list of sites noting which have PAPIs, etc (e.g. Edwards runways 33 and 18L do not for the STS-114 example--interestingly, JSC-48029's Edwards AFB section specifically calls out that "PAPI and Ball Bar lights can be moved with 24-hours notice and will be configured to meet mission requirements").
So there's at least an acknowledgment that the lights are angled for the Shuttle glideslope. Per the 1991 revision of JSC-48029 above, not all the alternate fields had PAPI lights (e.g. Amberly, Australia, the alphabetically-first ELS listed, is marked no PAPI, no Ball/Bar, no MLS). If they were available, adjusting a PAPI light doesn't seem particularly hard; from the Flightlight PAPI Manual:
For each 1/4 turn executed on the nut on one side, turn the nut on the other side 1/4 turn in the opposite direction. This will keep the lens center at the same elevation at all times during adjustment. Recheck both points. Position the proper aiming block on the edge of the light box for vertical alignment. Place the spirit level on the aiming block. Adjust the both rear adjustment jacks to bring the spirit level to center. Next, tighten the bolts holding the pivots. These are accessible underneath
the unit at the forward corners. Tighten all nuts securely. Recheck the horizontal adjustment and adjust as required. Recheck the vertical adjustment, then tighten all nuts on the new pivot. Last, place the level on top of the tilt switch. Adjust the tilt switch until the spirit level is centered. Tighten the bolts to hold the tilt switch secure. Replace the cover on the light box assembly.
Presumably if you had been voluntold that your PAPI-equipped airfield was now a Shuttle alternate airfield, provisions to aim the PAPI lights for the steeper glideslope could have been made (including ensuring the jacks could be adjusted that far, having an appropriate aiming block, etc). But maybe, since Amberly, Australia 15/33 does have PAPI lights (though did it when that copy of JSC-48029 was released in 1991?) maybe normally-angled PAPI lights are simply listed as "PAPI: no" for Space Shuttle purposes.
ILS is a different story. Per NASA SP-504: Space Shuttle Avionics System, Section 3-07:
The predominant navigation aids in place at the time for the final approach and landing phase were the FAA ILS and the USAF ground-controlled approach (GCA) system; however, both the performance and the coverage provided by these systems were deemed inadequate for the type of approach to be flown by the Space Shuttle. The FAA was considering an upgrade to a precision microwave landing system, but no firm schedule existed. Precision microwave systems also under development by DOD would meet Space Shuttle performance and coverage requirements, and a variation of one of these was chosen, again modified to interface with the DPS. Triple redundancy was considered sufficient for this system also, both because of the short exposure and because the pilot could take over visually under most expected conditions.
So Shuttle ended up with a nearly-bespoke system, the Microwave Scanning Beam Landing System, and so did some of the airports it could land at, including Edwards, Dryden, the Shuttle Landing Facility, and the alternates in Spain and Morocco. Searching that copy of JSC-48029 is difficult but I've found at least one other MLS airfield, Yundum International in Banjul, Gambia (BYD). Elsewhere I've seen these referred to as "augmented landing sites."
- I don't think I've been able to answer what I think of as your main question, i.e. would glideslope indications be adjusted for the Space Shuttle orbiter during an emergency landing, just confirmed that specially-pointed PAPIs were available
- Shuttle didn't use ILS, it used a different system, so ILS adjustment is moot.
- Not all the Emergency Landing sites have the lighting; for example, Amberly, Australia