For a national ranking to be meaningful, it is desirable to include as many tournaments as possible, so that a form peak - or injury - at the yearly national championship tournament has only limited impact.
Typically, these rankings take into account the average or the best tournament results of the player. For instance, per §6 of the Indian Ranking System regulations, the ranking is determined by the sum of points gathered by the 6 best tournament finishes in the previous 52 weeks.
If a player plays less than 6 tournaments, all of their points count (§6.1). In theory, the regulation could be changed to scale the average points, but that would mean that a player who wins the only tournament they competed in would immediately rank #1, which is not desired.
Top-level badminton players like Saina Nehwal or P.V. Sindhu only play in the national championship tournament. The other national-level tournaments are not a challenge for them, conflict with international tournaments, or do not fit into their long-term training and rest plans; while competing in local tournaments would yield them small amounts of fame and money, it would severely reduce their chances at tournaments that really count.
The Indian regulations do take this into account:
5.1 Additional points shall be added to the points earned by a player as per Indian Ranking System under the following circumstances: The ranking points equivalent to one tenth of the points to the credit of a player as per latest BWF ranking list in the same event. (...)
As of writing, Saina Nehwal has 54720 points in the BWF ranking, which would comfortably give her the first in the Indian ranking on its own with 5472 Indian ranking points, easily before Anura Prabhudesai with 3247 points.
However, it seems these BWF points are not included on the Badminton India ranking website. Most likely, the additional points are only counted for entering and seeding in the national championships.