Interestingly enough, the way I understood the beacons was that they weren't even messages meant for anyone in the future. I know, I know, but bare with me here. After the dozen or so scientists were woken up by Vigil they sent out a signal to the beacons that was meant to warn any remaining Protheans of the reapers and show them about Ilos to give them hope (I guess they figured it was worth the risk or they were screwed anyways). The only reason Shepard could understand the Beacon's message was because he got the Cipher (which also allows him to understand Prothean because it effectively allows him to think like a Prothean) from Shiala. It was impossible to understand the message in the Beacon without the Cipher because it was coming from Prothean minds, meant for Prothean minds. The best you could get was that some serious shit went down and the Protheans got destroy.
So after they sent off the Beacon message they figured out the link between the Reapers/Citadel/Keepers and jumped through the conduit to go mess with the Reapers plans; remember, there is no food and very little water, if any at all on the citadel. They get there and tinker around with the Keepers, I'm going to assume they could mass update otherwise they would have missed some Keepers, and eventually figure out the code and either alter it slightly so it fails or just deleted that part of the Keepers entirely. They're intent (to what I understood) was to protect the less evolved species they had been studying and to trap the Reapers in the dark space forever. They didn't warn us because that wasn't what their mission was. Also remember the Keepers have a self-destruct mechanism (yay acid!) to prevent the Protheans from doing exactly what they were trying to do, that couldn't have helped. Their mission was to make it so we wouldn't need a warning at all and could just go on existing without knowing. They tried to break the cycle entirely, unfortunately they failed.
I think what it comes down to is how long it would actually take to hack into the Citadel and then alter the programming that a far advanced AI race had laid out. Then even if they had of left a message there isn't any guarantee that it would have made it through the 50,000 years or so before the Asari showed up on the Citadel. I mean, with Keepers doing around doing their Keeper stuff and possible Reaper sub-routines messing around with any data stored on the system any message left on the Citadel would have been destroyed. If they even had the time/energy left to leave a message at all after altering the Keepers.