Is there a difference in using the subjunctive “να” vs using “πρέπει να”?

Slight. As with Are να and ας translated identically when used with a first person plural verb in Modern Greek?, it’s mostly a nuance thing:

• ας φύγουμε: “let’s leave, how about we leave”: pretty weak sauce, gentle prodding
• πρέπει να φύγουμε: “we must leave”, strong implication that this is an external imposition
• να φύγουμε: “we should leave”: it’s by default a command, and the implication is that there is no external imposition to do so, it’s because you want it. It can be a suggestion, but it’s not as weak sauce a suggestion as ας.