Gnome's Papers and, of course, KDE's Okular sign PDF without a hassle. If you need to edit PDFs, too, MasterPDF [1] is a solid choice. Not quite PDF X-Change in power or Acrobat Pro in looks it is sufficient for daily tasks.

The real obstacle to digitally signing is bad support for Linux by the card reader vendors, as usual.

[1] https://code-industry.net/masterpdfeditor/