How is Section 31 funded? In Star Trek, money doesn't really exist, although there seems to be a finite limit to star ship production.
Section 31 is an autonomous clandestine organization, meaning they get their own resources by their own means.
Think of it as the clandestine part of CIA or any other similar agencies. CIA is founded by the government but also has clandestine $-producing ops of it's own, as it has been proven over and over again.
As Solan implies, S31 has sufficient contacts within Starfleet to access required resources and equipment when the situation demands it.
Also note, that excessive starship production from them would significantly increase the risk of S31's activities being discovered on a sufficiently large scale so that the Federation would of been obliged to take an official position regarding them.