Tags with several values are a well-supported feature in OSM. The recommended syntax is to have a semicolon-separated list. Your proposal of adding number to keys is not a generally accepted scheme. I only know of few tags for which this is an official scheme, e.g. 'seamark'  and 'inscription' in cases the 255 characters of the value are not sufficient.

Which "tools" don't understand semicolon-separated values in additional tags? As this is a major feature of many tags I'd argue that these tools are broken and need to be fixed.

Coming back to 'wikidata': There are 0 tags with a :N suffix in the database, but two dozen with several semicolon-separated values. 
Fixing / documenting issues in the wikidata database doesn't seem to be something that should be in the OSM database.