1. In "Broken Link", the Defiant
is surrounded by Dominion vessels. There was no danger to the Dominion from a single Federation warship. If Garak had managed to start firing at the Great Link from orbit, the Dominion warships would've blown her out of the sky.
2. In "Inter Arma Enim Silent Leges", the Bellerophon
is bringing a whole delegation of Federation officials to meet with the Romulan government at a conference. There's always distrust between the Romulans and the rest of the galaxy, but there's distrust
and then there's dysfunctional paranoia
. The Romulans aren't dysfunctional - they had no reason to bar an allied starship from their space. Plus it gives them the opportunity to inspect one of the newest models of Starfleet vessel up close.
3. Assuming you mean the episode "The Wire" and not the magazine Wired
, Bashir headed off into Cardassian territory on his own volition. What did you think he was going to do - book passage on a commercial flight? The Cardassians, as a government, didn't know or care about Garak suffering a breakdown in his implant. Bashir went to Tain because he
cared about Garak. There's no reason to expect the Cardassians would want to ferry Bashir to Tain. It does prove that a runabout can fly into Cardassian space unchallenged, apparently, by any border guards, but then, being a mere runabout, it's not a threat, either.