An indicator refresh would cause a check of the usage database if there
was a search active, as it could possibly change the ordering of the
search.  Though, it sounds like that's not the case here.

Not sure of the exact cause, but a work around would be to tell the HUD
to not save usage data so it'll only use an in-memory database:

  $ gsettings set com.canonical.indicator.appmenu.hud store-usage-data
false

Which would mean that the locking files wouldn't be checked as the
database is read.

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https://bugs.launchpad.net/bugs/998759

Title:
  hud-service frequently tries to accesses non existing files causing
  high disk/network activity

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