The publications who run the ads, etc. give huge discounts to the tzedakas and are lucky if they get paid at all in the end. So don’t even wonder about what was paid for the ads it should never be your daigah, because you never know if someone sponsored the ads, if they got a discount or if the publication donated the ad space.
As for where to donated money. Everyone need to support the mosdos or tzedakas that THEY feel and choose that are most important to them. If it is a hospital, a yeshiva, a bikur cholim. Whatever touches your heart, that is where you contribute the bulk of your tzedaka and where you should consider getting involved. You don’t choose a tzedaka by the size or quality of their ads.