Hitman games are, roughly speaking, puzzlers.
Deus Ex games also have an "approach puzzle" aspect, but are also exploration games with a living narrative.
Since I play to explore stories and have memorable experiences, Deus Ex is by far the better game for me. There's a dozen memories I have from the original Deus Ex that I can recall right now, but the only things I remember from Hitman: Codename 47 are the constant crashes, frustrating mechanics and a joke reference/easter egg from the mental patients: "a' ge mam?" ("Er det mam?" directly translates to "Is that yum/food?" in the way a toddler would ask their parent, referencing a Danish comedy sketch by GramseSpektrum.) The only reason I remember that is because my best friend kept saying it over and over.
In other words, Hitman is in my eyes, at best a novelty. I'm glad it exists, but I have my preference, even if they're not directly comparable.