By RAW: There's nothing suggesting that it would be recognized as the smite has nothing indicating that it gives away the fact that it's a smite. Being a supernatural ability means it doesn't have component costs and thus no check could be made to recognize a smite.
For house rule purposes: Yes, a Paladin should recognize the use of Smite. It's a skill they have, and as such should be able to recognize the ability being used against them. In 5e this isn't a question because Smite adds radiant damage. In 3.5 though it just punishes good/evil, but to such a small extent that it wouldn't be recognizable unless you add some flavour to the smite.
Example: Your smite damage doesn't apply to the physical blow (although that is still required to deliver the punishment), but rather punishes the player for their wicked/good nature. That means in addition to the regular attack, the smite hits for +x levels of paladin/blackguard against the very nature of the person, and thus gives away an indication of supernatural ability use.