LOL, somehow, I never run into this problem at the same scale as you. At most I've had about 20 of each agent type and that happened when playing as Seleucids I allowed my Eastern Satraps to rebel (resulting in many factions sending their agents into my territory). In most times: I have just slightly above my max.
The main reasons why I use agents: 1) to counter the AI's agents; 2) to push regions of my allies into rebellions [an authority focused spy + a dignitary work really well]; 3) crowd control (of AI armies) - any successful agent sabotage action will stop an army from reinforcing.
Money is usually not a problem in TW even on legendary difficulty (except at the campaign start, but then, agents are not a big problem either).
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