This question is more of a question on whether boycotting can be an action of effective altruism, rather than a particular cause.
Pessimistically, it seems that there is no way to stop factory farming - and that veganism is not really that effective at all. Furthermore, boycotting companies like Nestle does not seem to make any sort of difference into the atrocities they commit.
As an EA, should you not care about boycotting?
This is just a quick answer to point out that veganism (which you mention in the question) is a bit different to other kinds of boycotts.
In a conventional boycott, you refuse to purchase certain kinds of products until the organisation(s) who sell them change their ways. I don't know much about how effective those kind of boycotts tend to be (although I think there are some famous examples of where large scale well organised boycotts seem to have produced some powerful results, e.g. montgomery bus boycott).
But veganism isn't just about pressuring organisations to make some policy change. You don't need large numbers of people taking part in order to have an impact. Each individual vegan who stops buying animal products will lower demand for animal products, and therefore reduce the number of animals who are raised for food (in expectation). It's not a binary "stop factory farming" or bust. Every extra vegan reduces the number of animals being raised on farms (in expectation).
But boycotts where you are trying to make a policy change require mass organization then?