There are two classes of people who can deny you access to aircraft: (1) airline employees (gate agents, check in agents) and (2) TSA inspectors. No one at an airport will know anything about EBCDIC, but every single airline employee will know about the fact that they're crappy mainframe system isn't smart enough to handle uppercase characters, let alone spaces, hyphens, umlauts, accents, etc.

As for TSA staff, it is important to realize that this EBCDIC issue is not a problem that only affects one airline: it affects almost every single airline, including all flag carriers that I know of. The airlines have a pretty tight working relationship with TSA; note that they send electronic messages to the TSA describing their customers when people book tickets and just before departure so as to give the TSA the opportunity to prevent them from flying. Given that tight relationship, I'm pretty sure that the TSA knows a great deal about the limitations of EBCDIC and has informed their staff about the limits of what a boarding pass name field can possibly represent.

Keep in mind that screeners will let you fly even if you have no ID on you.