If you want my advice: Get a masters but don't focus exclusively on aviation.
I was a furloughed airline pilot in 2001. Had a BSc. in Aeronautics from one of those aviation universities (read pilot factory...at least I didn't get my initial training there). Got furloughed and took a Masters in International Economics. Passed up on returning full-time to the cockpit and managed to get a PhD with an airline that paid for it. Now I teach aviation management and research in aviation. You can learn the same, if not more, if you do a Masters that is not focused on aviation solely. Get a Masters in something you are interested in, otherwise you won't finish or you'll hate the experience.
If a Masters in aviation is your goal, then go for it. However, if you want to complement your skills then a broader Masters, such as in management in general, may be more applicable. Airlines are not staffed with people holding specific aviation degrees.
I can only recommend that people with experience or school from outside the industry be hired as they bring a fresh perspective to the table. You're much more valuable if you have some operational or airline experience, but have done some schooling in other fields. Otherwise, you may just end up regurgitating what everybody else knows.