This bug was fixed in the package sni-qt -
0.2.7+16.04.20170217.1-0ubuntu1

---------------
sni-qt (0.2.7+16.04.20170217.1-0ubuntu1) xenial; urgency=medium

  * statusnotifieritem: reset app usertime on activation to ensure
    compiz will raise it (LP: #627195)
  * IconCache: get the proper theme path based on the fact we're using a
    themed icon or not (LP: #1600136)
  * fsutils: always use $XDG_RUNTIME_DIR if it's set for saving icons

 -- Marco Trevisan (TreviƱo) <m...@3v1n0.net>  Fri, 17 Feb 2017 01:14:24
+0000

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https://bugs.launchpad.net/bugs/1600136

Title:
  App indicator does not show icon for Qt apps or with custom icons

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