I'm not sure of the name of the tense for "were to be" and I couldn't find it in my quick search of grammar sites. But the meaning is of a past plan or intent to do something in the future. Normally the understanding is that this plan was never completed.
"We were to be married in June." Our plan was to get married in June, but for some reason we didn't.
"I was to get the job when Bob retired." The plan was that when Bob retired, I was going to get the job. But then something interfered and I didn't.
This tense is also sometimes expressed with the words "was going to".
"I was going to eat that slice of pizza." My plan was to eat the pizza, but then something happened, like maybe someone else got it first.
It's a complex tense, and the sentence is made a little more confusing because it's combined with "believe", in the present tense. The idea is that the police believe -- present -- that the owners of the plants planned -- past, the plan was ruined when the plants were confiscated -- to use the plants to make ricin -- future.
As to your proposed variations: Well, let me simplify the sentence a little to discuss that. Let's leave out some extraneous stuff and recast it as, "They believe the plants were to be the raw material."
Leave out "to be": "They believe the plants were the raw material." This moves the using of the plants as raw material from a future plan to a past state. That plants were the raw material -- past. There is no future plan, it's already done.
Leave out "were": "They believe the plants to be the raw material." The plants are the raw material in the present.
Another variation perhaps useful to understanding is to leave out "they believe": "The plants were to be the raw material." There was a plan to use the plants as raw material. This makes it a simple statement of fact rather than a belief held by the investigators. (In context, the original sentence is saying that the investigators believed such-and-such to be true, not that it actually was true. The investigators might be mistaken.)