The way the agency is getting around the NI thing is they're taking it out of what they get from the client before passing the rest on to me.
Say the client is paying the agency £300/day for providing someone to work. The agency is taking their fee from the £300, and also taking their NI contribution from the £300, and giving me the rest as my compensation.
If I tell the agency I want the NI contributions to be covered, they'll increase the amount they charge the client, who might pick someone else from the agency who is cheaper because they've agreed to the lower rate.
I don't know how they're handling holiday & sick pay. I'm probably not going to be with them much longer, anyway.