Half-etched fiducials Vs through-cut fiducials
According to Seeed Studio, there are three options for fiducials on SMT stencils. Note what they say about half etched fiducials below:

No fiducial ---- No positioning holes required on the stencil

Etched Though --- Positioning holes that go all the way through the stencil. Useful for manually holding the stencil in a fixture for manual/semi-manual paste application. These should be specified in the files by the customer since exact requirements depend on the customers' own preferences.

Half Etched --- Holes that go half-way through the stencil. These are needed for some fully automated paste applicators. The diameter is typically 1mm and are added to the corners of the stencil by our engineers if not already designed in the files.

SOURCE: http://support.seeedstudio.com/knowledgebase/articles/1156336-what-are-smt-stencil-fiducial-marks