After short investigation... GDM implementation of clock-widget does not use format-string defined for time in locale. Instead it uses hard-coded, although translatable, format string for clock output.
Therefore for now problem may be solved by properly adapting translations of the original format strings for time and datetime. There are two in gdm.po:
msgid "%l:%M %p"
msgid "%l:%M:%S %p"
Date format string may be also of interest:
msgid "%a %b %e"
Better solution would be to use appropriate format strings defined in locale. Since there might be justification for current choice, I do not know how feasible it is.