Does a strobe light shield act like a wingtip fence [or better sort of vortex generator]?
It is a long structured question, I will try to keep up with the answer. As first I would like to cite some sources.

I compared both CS23 and CS25 looking for the certification requirements on the lights. They are almost identical. If you want to check them yourself the keyword you want to use is "Lights". The paragraphs of main interest are from 1285, to 1401, three pages in total. That said.


  I was told it is a shield to avoid to blind the pilot during night flights when the strobes are on.


The light on the wingtip in this case are both position lights and anti-collision lights, the strobing light you refer to.

The Position lights: are described in paragraph from 1285 to 1391. There are requirements on the shielding of them and the intensity of the lights from different radians as well as the colors of them, but none from an aerodynamic point of view. 

From a design point of view the shield should define some dihedral angles:



  (b) Dihedral angle L (left) is formed by two
  intersecting vertical planes, the first parallel to the
  longitudinal axis of the aeroplane, and the other at110º to the left of the first, as viewed when looking
  forward along the longitudinal axis.


  (c) Dihedral angle R (right) is formed by two
  intersecting vertical planes, the first parallel to the
  longitudinal axis of the aeroplane, and the other at
  110º to the right of the first, as viewed when looking
  forward along the longitudinal axis.


  (d) Dihedral angle A (aft) is formed by two
  intersecting vertical planes making angles of 70º to
  the right and to the left, respectively, to a vertical
  plane passing through the longitudinal axis, as
  viewed when looking aft along the longitudinal axis.



For the anti collision lights: 


  The aeroplane must have an anticollision
  light system that




  (1) Consists of one or more approved
  anti-collision lights located so that their light will
  not impair the crew’s vision or detract from the
  conspicuity of the position lights


  (b) Field of coverage. The system must consist
  of enough light to illuminate the vital areas around
  the aeroplane considering the physical configuration
  and flight characteristics of the aeroplane. The field
  of coverage must extend in each direction within at
  least 75º above and 75º below the horizontal plane of
  the aeroplane, except that a solid angle or angles of
  obstructed visibility totalling not more than 0·03
  steradians is allowable within a solid angle equal to
  0·15 steradians centred about the longitudinal axis in
  the rearward direction.



On the aerodynamics effect of vortex generator at the wingtip, I found a paper: Modification of a wing tip vortex by vortex generators. It is an experimental study without a wingtip device though. Citing from the conclusion paragraph:


  The results show that substantial redistribution of wake circulation can
  be achieved by the merger of the tip vortex with a co-rotating
  vortex from the VG with the core radius of the merged vortex increased by a factor of up to five relative to the undisturbed
  tip vortex.


The VG was though positioned at a $\eta =\frac{y}{b} = 0.2$ inboard of the wingboard. 

Summing up the comments above, and merging this interesting explanation from @Peter Kämpf on winglets, what I think (yes, it is an "opinion", but otherwise I would need to run some 3D CFD and/or a wind-tunnel test) is that:


There would be a vortex generated in certain conditions for sure. 
To design this device in order to avoid winglet stall separation would be quite a challenging task. The device its positioned very outboard which would make it be more or less aligned with the winglet. I think that the close span-wise coupling between he device and the winglet would make it hard for the vortex to develop in such a way to re-attach the flow on the winglet.