When I used to live in Brazil I used to refurbish/repair scratched dome ports.
The most common type of scratches are the ones so called "hairline".
They occur mainly on acrylic domes and although they are inevitable and easy to polish (it's a less than 1h job) the use of the cover in (or dirty with) sea water makes your dome much more susceptible to them.
I still don't have enough experience with glass domes (I have used mine for less than a year) but generally the only way to fix them is with a Credit Card (and a good one...).
On the other hand they might protect from bigger damages on entering/exiting the water.
One other thing that I have mixed feelings is when people rely on dome covers and BC clips to hold their domes.
I have seen (people contacting me for repairs) many an irreparable domes due to it hitting things while the owner was unaware of them (other divers tanks are my personal favorite) when it is clipped to a BC and covered... I feel that when you hold them it might be more work to do, but it is safer because you are always aware of their position.
Good Luck