My former agent told me my nonfiction proposal was "great!" Then he immediately sent it out to six large trade houses and three university presses. The only sign of interest came from a university press that had already published an earlier work of mine. It was listed in my author's bio. It didn't occur to me to say to the agent, "Oh, by the way, please don't send my proposal there. If I'd wanted them to publish my work, I wouldn't have bothered getting an agent in the first place" (which was also true of the two other university presses). It was embarrassing to get a call from the director of the press, whom I know well, and have to say, "Well, I'm really looking to place this book at a trade house." Should agents let their clients know beforehand where they are sending the client's proposal, or should clients spell out a problem like this? Or should an agent say, "I'm not sure that your book is commercial material, so I'd like to include a couple of university presses, too"? That would be a lot more helpful than "It's great!"
We've all done stuff like that. I once sent a hot diggety dog proposal to an editor cause I KNEW it was perfect for her. She'd just moved houses, was building her list, and we were going like gangbusters. Turns out one of the books the proposal cited as competition with some less than flattering words was...of course...published by this editor's new house. Ooops.
There's a lot I don't keep in my head. I try to keep pretty detailed notes. But if you don't want your book proposal to go to university presses in general or a press in particular, regardless of "should" , I'd advise saying something and putting it in an email too. I'd much rather feel stupid with a client if I have to feel stupid somewhere, than with an editor, and her boss, in a meeting.
I don't usually tell clients where I'm sending things ahead of time. I let them know post submission, and if there is any feedback.