Copyrighted or not, certification logos/seals are often recognized by their visual impact.
In my opinion, even if it is permitted by the terms of the certification, I would not alter their colors. Any variation of the default color setting could possibly imply it's not a legitimate seal.
For specifics on what may or may not be permitted, you would need to check the terms of each certification seal. Some may have explicit clauses stating you are not to alter the visual appearance of the seal.
In very broad, sweeping terms, not everything on a web site should match the overall color theme. Too much of the same thing could actually detract from the overall visual impact.