Why do you think civilian ships are allowed in. I would say evidence says otherwise, as Romulans were able to completely isolate themselves for a century and later again for about half a century.
Because the Romulans only isolated themselves from the FEDERATION. They apparently spent most of that time playing cloak and dagger games with the Klingons and the Cardassians.
More to the point, Starfleet is and has always been a sort of closed loop that doesn't interact much with the non-Starfleet operators of the galaxy. Part of this is because they primarily "explore strange new worlds" and thus have an inherent tendency to avoid places that have already been explored and colonized; the only times they ever operate near civilization is when something has either gone horribly wrong or is in danger of doing so unless they intervene. Mainly for this reason, civilian space traffic is usually pretty far below Starfleet's radar, and traffic in the neutral zone, doubly so. Starfleet officers have themselves taken advantage of this from time to time to get access to places that would normally be offlimits to them (in "Birthright" Worf actually charters a shuttle to take him to a Romulan prison camp in hopes of finding his father).
Moreover, it's just the political logic of it all. It's said that any violation of the neutral zone would constitute an act of war; that can't POSSIBLY apply to civilians, since Starfleet could in no way be held legally responsible for the actions of civilian captains outside of their chain of command, nor does that appear to be the point of a region of space called the Neutral
Zone. Neutral meaning it should theoretically be accessible by anyone, any time, for any reason; the only people who can't
go there are Starfleet and the Romulan fleet.