I know the metal humbucker covers affect the tone of the pickup but what about plastic ones?
Plastic will not directly impact the tone, although (depending on the design) it could affect tone indirectly by causing the pickup and/or polepieces to be be further from the strings.
In no case did it affect the distance from the strings because I don't usually have them very close.
A guitar tech here recommended them (plastic ones) to me as non-relevant to the tone.
There are good points stated above though.
But (depending on how you adjust the pole pieces) on a covered pickup the slugs will be further from the strings in relation to the fillisters of an uncovered pickup. Again, depending on how you adjust the fillsters.
True, but that would be true with no cover as well.
Most people tend to raise the poles because it just looks weird if they're sunk down in there. But the effect of raising them is the same either way -- makes the pu brighter.
Depending on the guitar, pickup, and material of the metal cover...he may or may not be right to recommend a plastic cover. What kind of pickup are we talking about? Is it already in the guitar? Does the pickup currently have a metal cover? What material is the cover made of? Does the guitar sound compressed, dark or muddy?
To my ears, A good quality cover doesn't have enough tonal impact for it to even be an issue. I usually just go for aesthetics. Of course if your guitar is voiced really dark or bright, it might be more of a concern.