It is a matter of discretion of the employer. Though it is not mentioned explicitly in the post, there is a possible inference that all those employees rejoined duty on the 16th. Similarly, another inference that their absence is not an uninformed one also becomes possible because of the usage of the term "absence " and the mention of marking them absent for want of leave at their credit in your post. In the absence of any leave to their credit, certainly the leave applied for should be treated as leave on loss of pay only.
Since these holidays actually fell in between the spells of their absence, they ought to have applied for permission to avail of the holidays in their leave applications. Otherwise, in my opinion, they would merge with the period of absence resulting in loss of pay for such holidays too.
Regarding LOP, I have one doubt .
If employee don't have Leave balance, if he/she took continuously 15 days leave, it should be a LOP. But.. if , that days compulsory holiday will come , we have to pay them holiday payment or not.
Whenever an employee goes on LOP for a continuous long stretch whether upon due authorization or unauthorizedly, the holidays, if any falling in between automatically merge with the LOP. Not obligatory to pay salary by segregating such days from the leave period.