[mswen]

From this comment it seems you are intending to pursue the masters while working. So the opportunity cost is not lost salary. Your opportunity cost would be measured more in time and stress. You will be giving up social time. If you are single and don't have children and are young enough that the masters degree has time to payoff, then I would encourage you to go for it.

Also, since you really enjoy both theory and hands on coding you are well situated to get maximum benefit by applying theory to real problems.