Mine did the same thing When I had about 18k, putting them into army's caused it to slow down to about 1 frame per second, lasted about a minute. Then crash.
Just for kicks, I loaded a save game, crushed the AI at 14k, then hit keep playing until I had about 20k frigates and told them all to attack move at the same time. It crashed. Very sad.
So, you're not alone. It was fun watching brutes destroy some juggernauts.
My hardware is an Nvidia 1080 TI, Intel 8086k, 64 gig ram.