Reimbursement paid to employee attracts sec 40a(3) or not?

No. It won't. Because practically u will debit the expense or asset (or anything for which ur employee paid) and credit the employee account. Then while paying to ur employee, u will debit employee a/c and credit the bank account. With this accounting in books read with Sec 40A(3), u as an Employer didn't paid or incurred any amount in cash. So there is no prob for u

It will be treated as indirect payment through your employee. As expense bill is in name of company, it will be considered for 40a(3).