I guess it's because Allen originally hired him to be a bulletproof, but later states that his true intention was to make him his lover. If someone you don't even remember suddenly tells you they have always been in love you, it can make you wonder if they have any other ulterior motives, which is why Noah was so suspicious.
I think Allen didn't want to scare Noah away by confessing to him right away since it was made clear that Noah had an aversion or trauma of being confessed to, so I think that was the reason behind his facade of not caring about him. I also think that he shot him so that he would know that he was different from the others he previously worked for, since Allen did not confess to him even after Noah died.
It was said that Allen saw Noah on television as an orphan being taken into an orphanage so maybe he fell in love at first sight, though it's pretty unlikely. It was also implied that they had met before but Noah has no recollection.
Besides all this, Allen still does seem pretty suspicious because he does not explain exactly how they previously met each other and how he came to love him. But Allen does seem to cherish Noah because he never wants him to get hurt and is willing to get hurt for him.
Anyway, this is just my interpretation, I still don't exactly know Allen's true intentions lol.
How is it that Allen and Noah are so in love, but Noah has little reason to trust Allen? Not saying he shouldn't, but Allen hasn't shared the reason he knows him or how he even knows him. If Allen had already love Noah, then he wouldn't have killed him first thing, right? During their first meeting, he also acts like he's never met or cared for Noah, which could be an act, but it also can make one think that he had fallen in love after Noah's wake up, but claims to have loved Noah long before. I don't know if this is confusing, if I'm confused, or if I'm completely missing something?
Basically, can someone make sense or this very odd relationship? (Not that I dislike the characters or story, I'm just dumb.)