This is not specific to only Durga or Devi. Other gods also have the mantras which depict as slayers of demons. It is a symbol of their attribute of destruction of evil and saving devotees from evil.
Names of devatas have more than one meanings. Durga means unconquerable. So, when we chant "Om Durgaye namaha", we not only remember her slaying Durgamasur, we remember that she is unconquerable and saves her devotees when prayed.
Worshipping the gods using such mantras will not mean that we are worshiping or remembering demons. The mantras clearly says Mahishasura mardinyai namaha which means "Om, I bow to the one who slain Mahishasura". If these mantras are chanted wrongly, that is another case.
For Vishnu or Krishna, there are many mantras which show that they have killed some demons. One of the famous names of Vishnu is Madhusudana. The meaning is "slayer of Madhu". There is a mantra Om "Madhusudanaya Namaha" meaning Om, I bow to slayer of Madhu. This signifies the attribute of Dushta Shikshana which is also a duty of God. There are many other names in the Vishnu Sahasranama and other stotras like this. Many rituals and sevas are performed in temples chanting these mantras.
Shiva is called called Gajantaka meaning the one who slayed Gajasura. Other gods also names like these and mantras associated with such forms.
So, saying there are no mantras for Vishnu, Shiva or other gods where they are said to kill demons is not quite right.