This appears to be a very unique handling of multiple web pages with no specific year by the same author. Are these rules specified somewhere?
I don’t think that EndNote has a way to do this, and am not even sure why or how the dash itself is specified. Since it is designed to define a year followed by the letter, with no punctuation, I assume it is trying to separate the period from the letter. The requirement to put the letter in this instance, in parentheses is not an option. You might provide the instructions that specify this in the “Suggestions Forum” here to alert the developers to this requirement.
Meanwhile, I can only suggest that prior to submission, you might make a copy, unlink fields on the copy and search for n.d.- and replace with n.d.( and add the other close parenthesis manually, or search for each letter n.d.-a and replace with n.d.(a) and n.d.-b with n.d.(b) etc.