I agree with mainecook. I usually salt my beans when I soak them. When I forget, I salt them when I cook them. I have never noticed an adverse effect. I don't cook them with tomatoes so I can't speak to that. Sometimes I think we end up with old, geriatric beans and there's no bringing them back. It happened to me recently. I ate one serving and tossed the rest. Crunchy beans make me cranky.

Sometimes you get a batch of old beans that grew when dinosaurs roamed the earth. And the nothing, but nothing, can get them to soften in a reasonable amount of time!