Well, it seems everyone I talk to has a slightly different idea of how things are working at present, what flags are available, etc. I PM'd Bobboau because Mantis lists him as taking care of something relevant, but he didn't seem to know much more than I did, and suggested I post here.
Here's what I think I know:
By default in the code, beams totally ignore shields.
The command line option -nobeampierce overrides any flags and the default setting to make beams have to take down shields before they can start damaging hull, just like any other weapon.
The weapon table flag "no pierce shields" does the above for a single beam weapon.
A mission flag, "pierce shields", can be set to make any weapon pierce shields. This overrides "no pierce shields" on beams, but not the command line option.
Not so sure about:
Some say that by default beams ignore shields below a certain number of shield points and hit shields above that number. I find this suspect because no one knows what that number is.
Other sources indicate that default is for damage to be done simultaneously to shields and to hull. This may not be the code default, but a default mission-making option in FRED.
Also, do any of you know of any code that could make a specific ship (mission or ship table option, whatever) invulnerable to shield-piercing weapons (much like -nobeampierce does for all ships), or how difficult this would be to implement if I could rope some coder into making up a special build for a mod? I ask this last question because I want to know if it's worth bothering to ask anyone about doing it.