I'm a new Evernote user, and can confirm that this issue still exists. I had a lengthy support request, and the final (and very unsatisfying) conclusion was that there is nothing I can do other than accept this is an ongoing issue. The support stafff just said that the engineering team is working on it, but that there is no ETA for a fix. Given that this issue goes back to 2013, I won't be holding my breath.
However while I was doing a manual check between Evernote Windows and Evernote web, I found a nifty solution to force a tag sync. I estimate that about 20% of tags on my Windows Evernote had tags that either didn't exist on the web, or were not fully tagged on the web. By that I mean tag1 might show 20 notes on the Windows client, but only 3 notes on the web one. To fix this I was manually editing each note (entering a space, for example), and this generally forced the tag to sync. But it was slow going. So I worked this out instead:
Log-in to Evernote web.
Create a new tag (e.g. temp1) on Evernote web.
On Windows Evernote, select a bunch of notes that have some issue with tags. Alternatively, just select all your notes.
Add the temporary tag to those notes.
Refresh Evernote web and see if it has fixed the issue.
If not, create a new tag (temp2) and apply it again.
Repeat the sync and refresh.
I had some good success with this. It didn't robustly fix all issues first time, but I was able to mass update 100 notes or more at a time using this method. In future when I want to force a tag sync I will just apply temp1 to all of my notes, and then go through my hierarchy of tags, comparing between Windows Evernote and the web one, and check how successful it was.
::rant:: By the way, this really sucks. It also sucks how printing still doesn't work nicely in Windows, again years after the original issues have been reported. ::/rant::