Methylene Blue is harmless to fish eggs and fry; so think would not harm tadpoles. It's weird they are "disappearing" since imagine you check several times a day and do not find bodies.

Tadpoles need lots of food and water quality is an issue since large water changes that alter the water chemistry could harm them. Foam filters are good since when cycled, will help reduce ammonia and nitrites. Also, tadpoles will pick out food off them (rotifers, etc.). Good luck with remaining tads !