The original ClustalO tool can take nucleotide sequences as input. There is even an option to specify the sequences type. This should also be supported in UGENE:
1) Allow to align nucleotide sequences with ClustalO.
2) Add an option to specify the alphabet.
Both these items should be done for:
1) The ClustalO dialog called from the "Tools > Multiple alignment" menu
2) The dialog called from an opened alignment
3) The workflow element