Working with many non-profits, they're very careful to keep expenses below a certain percentage of their donations. Otherwise sites likes these cause them to lose donations.
Unfortunately this results in low salaries for employees which means the employees gain skills but can't afford to keep working there. The non-profit loses talent they helped build.
I know of some non-profits who have gotten around this by creating a 2nd non-profit where they receive donations just for business & administrative costs. Than use their 1st non-profit to say 100% of donations goes to our causes.
In reality, you should get to know your non-profits. Volunteer & help them out. Then you'll have a better understanding of how they use their money. Sometimes those high administrative costs result in a lot of value being achieved, even if the percentages don't look great.
Personally I'm a huge fan of a lot of community non-profits like local YMCA's if anyone is looking for a good place to start. I also tend to work with other small, local non-profits.
I think one ends up down a deep rabbit hole comparing different non-profits. In the end I think you need to find a mission you care about & a group that you believe does it well. I think the most important thing is that you are invested in the non-profit.
A local YMCA can provide very cheap after school child care & activities that keep kids safe, out of trouble, maybe a small meal & allows their parents to work. This can end up having very huge benefits directly & indirectly in the community.
GiveWell shows a lot of cost effective ways to distribute things like medicine & safety items. Plenty of awesome non-profits there.
I work with some small non-profits that pick & fund specific research at universities on childhood cancer.
I'm not sure how you compare different non-profits like that. Especially if you want to see the impact they have over N years, how that impact is spread or if some other larger issue needs to be addressed that's making a non-profits work pointless. GiveWell itself says it doesn't try to be a charity evaluator. They try to find a small number of really good donation opportunities for people.