Hello,
I work a lot with GPX files (I even have my own website for that). And honestly, I’m not sure what you mean by “ID column present in the attribute table.”
GPX is an XML format, so everything is stored using tags. Specifically, the name of a WayPoint is enclosed in <name> tags. If your GPX file contains <name> elements, these will be imported into Mapy.com as waypoint labels.
Maybe your labels are stored in some <extensions> tags instead?
I’d be interested in seeing your file – I’ll message you via chat.