Is the efficiency of poisonous colors decreased?

Using color damages a Sister's realm. The damage is smaller per point if the color is poisonous to her, and bigger per point if it is a favored color. The implications for farming are clear: infuse trees with poisonous color to mitigate realm damage.

What about combat? Aside from realm damage, is the power of the colors affected as well? Do ten points of a favored color have the same amount of attack power as ten points of a nature-friendly, poisonous color? Does the duration of golems or other glyphs depend on color type as well as the amount used?

Yes and no.

Imbuing glyphs with larger amounts of colour does make them more powerful/last longer. However, each glyph has a maximum limit, after which colour no longer increases its potency. Fortunately, excess colour is just returned to your palette, rather than being lost.

As far as I can find there is no released data as to what the maximum amount of colour per glyph is. I did find, however, according to a guide on GameFAQs (sections [7.02] and [8.01]), that the "Hawk" glyph has a maximum of 32. The author says they have spoken to one of the devs about a number of workings in the game (see section [9.00]), so I assume that this is where the information came from.

In regards to which colour is used, I can find nothing to say that a favoured/poisonous colour in different realms make glyphs more or less powerful. So I will cautiously say that the colour used does not matter. When realms take damage though, Brothers do become weaker anyway. they also have a colour wheel with a weakness, though this is not extended to regular enemies.