I know this is an old question and that an HTML page with multiple identical IDs is invalid. However, I ran into this issues while needing to scrape and reformat someone else’s API’s HTML documentation that contained duplicate IDs (invalid HTML).
So for anyone else, here is the code I used to work around the issue using querySelectorAll:
var elms = document.querySelectorAll("[id='duplicateID']");
for(var i = 0; i < elms.length; i++)
elms[i].style.display='none'; // <-- whatever you need to do here.