I agree it was a little...
(the rest of this isn't really spoilery if one has completed ME2 already, so I'll leave off the tags)
Regarding the nature of mass relays; if I remember this right from the codex, relays have some kind of stasis field that protects them from damage over time. This also makes them effectively impenetrable. As for the Citadel, it's stated that there are whole sections that are inaccessible and between the automated systems and the Keepers, the station essentially runs itself and automatically adapts to the needs of the inhabitants. Any initial suspicion would have eventually faded as several millennia of habitation proved the station to be apparantly benign.
It's also worth remembering that the Reapers are extremely advanced and intentionally built these things to be easily used but next to impossible to truly understand, so it shouldn't be surprising that they camouflaged much of their true capabilities. Additionally, give that the Keepers have a habit of self-destructing if interfered with, it's not much of a leap of logic to presume the Citadel or the Mass Relays might react similarly to an invasive investigation. In short, everyone's very happy that these things work and nobody wants to risk loosing them in a foolish attempt to poke around where they're not welcome.
As for Omega, I'm pretty sure the Terminus systems wouldn't react well if any of the citadel races decided to blow up the Omega-4 relay, taking their de facto capital and central commercial hub with it. The fact that in ME1 the council was so afraid of a war with the Terminus systems that they refused to send a fleet after Saren. If the mere appearance of a fleet is liable to set them off, think what a blatant act of terrorism would provoke. Aside from that, a LOT of money and trade moves through Omega and I wouldn't be surprised if a fair portion of that (officially or otherwise) flows right from the Citadel.
As for the Collectors, as had been repeatedly stated, they were very rarely seen, practically a myth and there were only unconfirmed reports of their ships transiting from the Omega-4 relay. Remember that the human colonies in the Terminus systems were independent and not part of the Systems Alliance. The colonists were warned that they were taking a risk by colonising planets outside the official protection of the Citadel Council. So when they start disappearing, it easy to put it down to pirates, slavers, or just hostile races.
Hackett is clearly a seasoned officer and trusts his instincts. Remember, he's the one that recommended Shepard to Udina for Spectre candidacy at the start of ME1, so right from the start the Commander had earned his respect.
As for Ash and Kaiden's reactions, I think it was mostly born out of shock that Shepard was still alive, that they had to find out second or third hand and that their Commander had apparantly betrayed the Alliance and defected to Cerberus. Hackett on the other hand is a big picture kind of guy. Plus if you romanced either Ash or Kaiden, you get an apology e-mail shortly after Horizon.
P.S. Here's and interesting bit of ominous foreshadowing for anyone that's completed Arrival; once everything is done and dusted, go back into the galaxy map and check out where the Normandy is suddenly parked...