I would like you to enable safe mode and then see if you still unable to see the upload add-on? If you able to see the upload add-on button after you enable the safe mode it means one of your 3rd party plugin causing this issue. I suggest you to disable the 3rd party plugin one by one and see which plugin causing this issue.
If you are using "Cloud", then you cannot upload addons. You need to go via your my.atlassian account.
If you are running "server" version, then you need to be an admin to upload addons, but even then, you really should use the "manage plugins" section to get it from the marketplace, rather than upload manually.
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