Beans are already dried, but it's certainly possible that baking them dries then further, or cooks them without softening. It's worth testing, for which I'd use chickpeas - I buy them in bulk, and they soften quite easily (plus I cook them on their own too make hummus while my other beans cook in chilli etc). I'd rinse them and put them on to soak once they've cooled a little, rather than storing them.
For reuse as baking beans I'd be concerned about two things: safety, and scorched beans giving an off flavour. The latter is addressed by not reusing them if they start to brown, and for the former, it's important to keep them dry, as dry beans keep indefinitely. If the beans are in direct contact with the pastry during blind baking, I'd rinse them briefly (to get any flecks of pastry off then return them to the cooling oven to dry quickly).