What´s the point then in putting it there. The Reapers moved into dark space because they hibernated and were vulnerable.
This decission might seem "unlogical", as another francises character would say.
Unlike the simple VI Vigil , the Catalyst did not anticipated this eventuality of someone hacking his system.
I do belief the Catalyst stays in hibernation just as the reaper fleet does, until the "ready to go signal" is sent by Sovereign. Sovereign's only purpose was to stay back and take some looks from time to time, if the civilisations of the galaxy have advanced enough to the point of possible erradication by their own creation, synthetics. Then he would start the harvest cycle by telling/contacting the keepers who "wake" the Catalyst that activates the Reaper fleet and the Citadel Mass Relay. Because preserving life in Reaper Form BEFORE it is destroyed by synthetics is his purpose, right?
But back to your question: Vigils knows that an organic other than prothean would find him, because it was written in his code by his creators.
An AI, like EDI or the Catalyst improves, rewrites, continues to write his code by gathering experiences, it learns, evolves. How do you learn...... one of the deepest learning effect comes from.... failure. We can/have to assume, that it never had experienced such an event before, yet it didn't feared or even anticipated as such.
There are hints, like Shep is the first organic to stand before it and so on.
To quote Garrus, they never saw it comming. And to minimize the possibility of beeing detected, no signals between Capt. Vanguard of Destruction and the Catalyst are send, unless the galaxy is ready to harvest, because they are indeed vulnerable, look at the damage the, compared to previous cycles, primite actual community did to them. Therefore the need the advantage of surprise.
And while that was a successful tactic in the past... 20.000 or so cycles..... why change a winning team. The catalyst is therefore right where he is needed most. In the center of it all on the citadel. This is what gets secured first by the Reapers. (Dumb thing they didn't shut down all mass relays when they moved it to Earth in ME3, just like they did in previous cycles which is the real plothole for me).
I am sure while the Catalyst was unable to perform any controlling actions with the protheans manipulation, it went from Hibernation to a vegetative state, it was able to communicate with Harbinger and the rest of the Reapers to activate and actuate them.