Not aware of any public guidelines.
However, here are a few tips on what I'm aware of standard industry practice.
Not many people use shear elements. 99% of wing-box-type models are shells (use CQUAD4s in Nastran; CQUAD8s look pretty but NASTRAN's are not as good as the CQUAD4s, which are a highly refined formulation developed over many years).
I've seen a global (whole-wing-box type) model with as few as 6 shell elements down the depth of the spar web. This seems a bit mean to me, but it worked for them.
For composite materials, smeared properties on MAT8s with PSHELLs are often used, rather than have a whole load of PCOMPs.
Often in a wing model things like the spar flanges and wing cover stiffeners will be modelled with bars (use CBEAMs not CBARs if you ever want to go non-linear). However, it's probably more sensible to use more QUADs these days; bars used to be used to save CPU, which basically isn't relevant any more. Stiffeners should be at least two QUAD4 elements deep (some say three). Generally element corner stress recovery should be turned on. These days this seems passably accurate in NASTRAN, but keep an eye on unusual geometry. "Strain gauge" bars (very low area and E to recover stresses along element edges) can used instead.
Offsets are often used, but make for trouble, as they can't be used with buckling runs or non-linear (though wing box type analysis is rarely taken non-linear). They also screw up structural-thermal runs. This is one reason not to use bars for stiffeners, as they should really be offset inwards. Un-offset bars for spar flanges is ok.
Usually simple outer mold line (OML) geometry is used. Things like rib feet are usually not modelled at the wing model scale, nor are fasteners. However, if you do have the time to put in some fasteners it can save a lot of effort later on.
For a wing, fin or tailplane box the leading edge is not usually modelled, and nor are the trailing edge control surfaces. Care is taken so that the TE surfaces do not pick up load due to wing bending. One exception to this was the DC10 and MD11 outboard flap; this had four flap tracks, and so it bent with the wing. Loads from things like flap tracks and engine pylons are usually applied as discrete forces at flap track and pylon attachment locations.
Things like access panels (e.g., manholes in the lower wing skin or upper tailplane) are not usually modelled. If they are, it's usual to connect them with fastener elements (CBUSHes in NASTRAN these days).
Often the basic aero SMT loads are applied using rigid elements (RBE3s) at rib positions. However, sometimes the actual air pressures are used, along with extra pressures or line loads for load on non-modelled surfaces (LE and TE).
Other tips: for linear runs start K6ROT (drilling freedom suppression) off at 1.0 or 10.0. Do not use AUTOSPC.
-RP.