Can we have beam secondaries/countermeasures/spawned weapons?
Beams use a different set of code than ordinary weapons so my off-the-cuff guess would be no.
does this mean that we can have countermeasures that spawn little shrapnel missiles?
You should be able to. However, my answer is in the same vein as the above - I can make educated guesses but I can't state for sure. There's a thousand different ways you can set up weapon variables and obviously I didn't test them all. The more reliable thing to do is to create a new modular table
wpntest-shp.tbm#Ship Classes
$Name: GTF Myrmidon
$Countermeasure Type: GTM-10 Piranha
#End
load up a mission with the Myrmidon, and test it out (by launching a countermeasure). Note that I pulled the Piranha name from the wiki, not from the tables, so it might not be correct.