Do the L1 applicants have to file taxes here in US? Or can they file their taxes in India?
Is there a mechanism via which their tax liabilities are optimized(maybe part of salary or compensation be paid in India rather than US or vice versa, if that helps)?

Income earned while physically working in the United States AND from a U.S. source is subject to U.S. income taxes, whether you file as a resident or non-resident alien.

To give more concise guidance, we need to know how long you have been in the U.S. and when (if you know) you will be returning to India.