Can enemy ships have Augments?

Yes they can have augments. The only ones I've encountered are:

• Zoltan shields (obviously)
• Rock Plating (most rock ships have this)
• Engi Medi-bot Dispersal (I've ran into several torus class ships with this augment).

I've run the medi-bot augment several times where their crew was healing while outside of their med-bay, which implies that they have that particular augmentation.

I have not encountered any ship with zoltan shield bypass yet, but I do not play the zoltan cruiser that often to know for sure.

It is a flavor text only. It is worth noting that bypassing the Zoltan shield augment only exists in the AE, but that flavor text is in both standard mode and AE. See z-'s answer for remaining details.