In football at least, Nepal in the mid-2000s did very well in youth tournaments, but that was because the Nepali team was results oriented while other teams were much more development focused.
Results in youth tournaments are not always a good indicator of the strength of youth football in a country as different countries have different objectives for tournaments. For example, Japan usually sends a local school team to the AFC Festival of Football. On the other hand Nepal's U13/14 team comprises of ANFA Academy players that have been living and training together for 2/3 years! They play to their strengths and always try to win, while more mature football nations might take a long term approach and choose to work on their weaknesses and sacrifice results. (And there are some other issues in play which I rather not discuss publicly).
At the end of the day 40, 60, 80 or even 100 kids training in a sole football academy is not going to take Nepali football to the next level. We need tens of thousands kids playing organized football under the supervision of competent coaches. That can only happen if ANFA, clubs and local communities work together.