There are over a million charities in the US alone. GiveWell currently has (around) 5 full time staff. If GiveWell were to investigate every charity this year. each staff member would have to investigate over 500 charities per day. Moreover, doing comparison of even two charities can be exceedingly tricky. I spent ~ 10 hours a week for five months investigating the cost effectiveness of school based deworming and I still don't know whether it's a better investment than bednets. So I strongly disagree that GiveWell shouldn't use time saving heuristics.

Aren't the numbers here a little specious? There may be over a million charities (is this including nonprofits which run social clubs? there are a lot of categories of nonprofits), but we can dismiss hundreds of thousands with just a cursory examination of their goals or their activity level. For example, could any sports-related charity come within an order of magnitude or two of a random GiveWell approved charity? Could any literary (or heck humanities charity) do that without specious Pascal's Wager-type arguments?

This isn't heuristic, this is simply the nature of the game. Some classes of activities just aren't very useful from the utilitarian perspective. (Imagine Christianity approved of moving piles of sand with tweezers and hence there were a few hundred thousand charities surrounding this activity - every town or city has a charity or three providing subsidized sand pits and sand scholarships. If a GiveWell dismissed them all out of hand, would you attack that too as a heuristic?)

Notice the two examples you picked - deworming and bed nets. Both are already highly similar: public health measures. You didn't pick, 'buy new pews for the local church' and 'deworm African kids'.