The -ms macros do in fact allow equation numbering (as I discovered much to my relief the other day, when writing up an article), but this is not mentioned in either groff_ms (7) or the info pages on -ms.
The manpage should read something like: .TP .BR ".EQ [\fI\,align\/\fP|\fI\,equation label\/\fP] [\fI\,align\/\fP]" " and " .EN Denotes an equation, to be processed by the .I eqn preprocessor. If the first optional argument is .BR C , .BR L , or\~\c .B I , it will be considered to be an .I align argument, to center (the default), left-justify, or indent the equation respectively. Any other argument will be used as a flush-right .I label for the equation. If the first argument is a .I label , then a second optional argument may be used for .I align . Robert.