Strain gauges are still the most reliable way to assess the strain and also (provided modulus is known reasonably accurately) stress.
Sandwich panels usually have simple sheet skins of a fairly uniform thickness or a thickness which changes in a known way. Because the core also tends to be a consistent thickness the bending moment in the panel can also be assessed from surface gauge readings.
I have assessed four point bending of a sandwich beam with various repairs on it. Gauges were used on the unrepaired area of the central span at least half the beam width away from the end of the repair and the end of the central beam span (it should have been at least a full beam width but there simply wasn't room in that case). They were put on both skins; the skin modulus differed in tension and compression, which should not be ignored (usually analysis crudely uses the average of T and C). We also put gauges near the edge of the beam in one place to check strain and stress distribution over the width. We wanted to check the in-plane failure stress that the repair broke at to compare different repair types. The gauging worked well for assessing this.
A metallic skin may have its thickness adjusted by chem-milling and it's important to avoid gauging a skin above a chem-mill step—I have seen this careless idiocy committed on a flap skin. A laminated skin may have a graduated thickness and while it's normally easy to avoid a rapid change in thickness (might be 10:1 in places), usually it is possible to avoid ply steps in more gradual thickness changes. Small foil gauges can be about 1/16th of an inch long (1.5 mm) although usually for cheapness and accuracy they are about 1/4" (6 mm). Triaxial rosettes are a bit bigger and enable recovery of two direct strains and shear (cheapish ones are 1/2" across—they tend to be three gauges in either an equilateral triangle or a right angle with one in the middle at 45°).
Foil gauges can be used for dynamic measurements at several hundred or even several thousand Hz and can be used in impacts over times of a few milliseconds and give a useful history of the event (subsonic types of impact, not ballistic).
Optical strain measurement is coming on fast. We have used it (from GOM) and it seems it can rival strain gauges for both accuracy and sample rate. Soon it should surpass them if it hasn't already. Setup issues exist for both but are very different. The GOM system seemed to be able to sample an area about 20 mm across but that memory may be unreliable; the system may be improved anyway of course,
Usually we assume that with a sandwich panel the in-plane strain doesn't vary through the skin thickness but if necessary it can be allowed for with the usual engineer's theory of bending distribution of strain through the panel thickness.
It is possible to put a gauge in the inside of a sandwich skin but this has obvious problems (relieving the core in way of the gauge and its wires and getting the wires out and incorporating the gauge in the panel manufacture) and usually isn't done; well, I have never seen it done, although we've thought about it. Maybe someone else has seen it done.
So, gauges measure strain over an area somewhere between 1.5 mm and 12 mm across and you can usually at least estimate skin endload and panel bending from that, and if it is a panel rather than a beam, full biaxial strain and shear can be recovered.
With composite skins it is assumed with reasonable accuracy that the surface strain isn't affected by the orientation of the surface ply. It may be necessary to prepare a simple (but big) 3D FE model at the ply level to convince people (and indeed yourself) of this.