My theory:
Beams cost (nothing cannon confirms this, but I didn't find anything against it).
Shivans rely on numbers.
When adding the two together- I come up with the idea of Shivans having different fleets for handling civilisations with different 'threat levels'.
In FS 1 the Shivans gave the GTA and PVN a low threat level- they lost 1 fighter during the first days of combat, killing cruisers and whole squadrons themselves.
The called in capships were the cheaper type, with no beams, and the Shivans held the beam-equipped units in reserve or in some other conflict.
To make sure that the Terrans and Vasudans get pwned quickly, a battleship with 2 huge beams was sent for breaking through defense lines and planetary bombardment.
The Shivans also decided to send a shield equipped capship, after noticing that Terrans and Vasudans have no weapons to counter heavy shielding.
So the Lucy was selected as flagship.
The plan failed, and the Lucy was lost in some 10 minutes of battle, attacked by a group of fighters.
After that, the Shivans officialy claimed the Lucy class obsolete and developed a new, huge-@$$ ship.
Then came FS 2. The GTVA got a 'high' threat level since the Shivans remembered their epic @$$-whooping from Alpha 1, and ships with beams were called, with a Sathanas en route to work as flagship.
The GTVA made a huge mess in the Shivan Nebula before the Sath appeared, forcing them to use units retired even in the FS 1 era, now serving as reserve and patrol ships (my little theory on why the SF Aeshma was so crappy compared to the Basilisk). The first Sath was also extinguished by a surprisingly huge water gun, so the Shivans gave the GTVA a 'F***ing High' threat level, and called the rest of the fleet.
In order to show the GTVA that they suck, and that destroying jump nodes when a fleet of jugs is assembling sucks too, Shivan command decided to test a new invention. A mechanism that would reactivate collapsed jump nodes by some ghey magic tricks the GTVA knows as subspace rifts.
Obviously, the 80 jugs set the rift generator power level too high, and instead of making the star artificially heavier (to create a large enough gravity well for a spontanous subspace node creation and recreation) it went KABOOM. Everyone, but those who noticed the plan isn't working and warped out, was smoked.
So today, post FS 2 we have a whole bunch of angry Shivans, working on a new master plan to open that can of whoop@$$ on us. Untill they will be absolutly sure this plan is perfect, they won't bother to come, and will concentrate on wars elsewhere instead.
Nodes are bottlenecks and with good blockades, you could make the shivans bleed..heavily. Also, a allready established system would house more fighters than several fleets - just think of all the room on planets/moons for fighter bases.
Gives me an idea: disable a Sath at the entrance of a node, and watch all the others that are already in subspace and can't turn back crash into it.