Electroporation disrupts cellular structure, especially the lipid bilayer, allowing molecules that are normally only outside the cell to move to the inside and vise versa. The effects of this will be quite variable depending on the local chemistry during (and for some period after) electroporation. Since relatively large molecules can pass through the membrane, electroporation techniques have been used for gene therapy and other transdermal drug therapies very successfully.

With all things though, there is a dark side. Careful cleaning of the skin surface is required to prevent the penetration of unknown chemicals into the cells. The possibility of transporting pathogens and carcinogens should considered carefully. Careful control of the osmotic environment is also important since over hydration may cause delamination of the stratum corneum.

Most facial electroporation devices have a very limited penetration depth and are considered inherently safe when used as directed by the manufacturer. Since pulse widths, pulse shape, and peak voltage probably vary between manufacturers, some of the potential side effects may be manufacturer dependant.

The most likely side effects of over use will be neural stimulation (resulting in pain and muscle stimulation)  caused by a reduction in the resistance of the stratum corneum and a reduction in the barrier function of the stratum corneum which could cause the skin to be more easily irritated. Disorganization of the stratum corneum may also lead to transepidermal water loss.  All of these should be reversible by discontinuing use of the therapy.

My final suggestion: whenever you are doing something that permeabilizes your first defense against external pathogens (your skin), you should use caution.