That far in the future and they forget the "Cut" and "Paste" commands

[Lazoriss]

This is actually touched upon heavily in-game, especially at Theta.

People were committing suicide right after their ARK scan in the hopes of having a single stream of consciousnesses that continued living on the ARK. The thing is, the loophole is merely an illusion. No matter how quickly you kill/delete the original brain, there will be an overlap in time. The new mode of conscious thought is a copy. A perfect copy, maybe, but still its own entity.

At Omicron, Catherine copies you into the new body. She knew that there was going to be two of you, but didn't tell you or "delete" diving suit Simon right after the scan. I can't say for sure why she didn't. But she is entirely reliant on Simon in launching the ARK, and we see her hiding information from Simon in fear of upsetting him and making him change his mind about aiding her. She might have been scared of Simon's reaction if he found out she had essentially killed him. Draining the battery wasn't instantaneous, so she couldn't hide killing the older personality. She leaves the decision up to you.

I have thought about how this works at the end of the game as well. It would have been interesting as an alternate ending. You could confront Catherine about the copy mechanic and request that she drain your battery during the ARK scan. You could indulge in the illusion of a single conscious existence continuing on the ARK, while not having to leave Power Suit Simon stranded at the bottom of the sea. The player would still have to deal with the fear knowing that you would still die in that pilot seat, just like the Simon at Omicron (if you decided to kill him).