NIC

Only the amount paid above 45p per mile would be included

What is the reason for that?

Tax is not a subject where every rule has a why! The rules are created by people - different people may create different rules. Here however it would be otherwise easy to avoid Class 1 NIC by simply reducing the salary and instead paying a hugely inflated mileage rate. It's a cash payment made above the exempt benefit level it is therefore not only chargeable to income tax but also to class 1 NIC Going forward at this level - I advise you to learn the rules rather than asking why.

Is it compulsory to deduct employment allowance while calculating class 1 secondary

Only if calculating the TOTAL amount payable by the employer for all employees - you do not deduct when simply computing the amount payable in respect of one of the employees