After equipping an addon or two to your ship, while docked with your capital ship, the addon slots will disappear. You can't configure your addons anymore until you undock and then dock again.

Example:

This happened at one point to me too, but instead of a capship it was in Latos N-15 station. None of the ships were showing their addon slots for a minute or two, but then it got fixed on its own, so I didn't bother reporting it.

This will be fixed in today's client patch.