If this is the case, its may hamper your prospects of justifying your actual salary to your next employer as there is no valid proof of salary being paid or taxes deducted.
(i) To reduce the existing threshold of cash payment to a person from twenty thousand rupees to ten thousand rupees in a single day; i.e any payment in cash above ten thousand rupees to a person in a day, shall not be allowed as deduction in computation of Income from "Profits and gains of business or profession";
it says a company can pay in cash to one individual Rs. 10000 in cash in a day and it is perfectly legal to do so. But for an employee, it would be difficult to show proof to next employer because there wont be any bank pass book entry or copy of cheque. So it is better your salary is credited to your bank account or a cheque is given to you for your salary.