It really seems to me that the decals that the local guys have are all meant to be peel and stick over the ones already there. This would be the only way to preserve the color.
Ah so you are talking about replacement art for the playfield.
FYI: What is on the playfield original is not a decal. Its screened INK, the entire playfield is screened. So putting on a decal is not equal to what is on the playfield from the factory.
There are many problems with insert decals:
1. Most of the time they are not accurate
2. They are not completely opaque
3. They won't fit the insert size wise
4. They are thicker than the INK on the playfield.
You will find even if you can get the decal onto the playfield it will sit above the surface of the playfield a bit. That is because the substrate is thicker than the ink. The only way to get it to sit level with the playfield is to lower the insert. That is easier said than done.
Back to your original question. Is it common practice for insert decals to not have the colored portions reproduced? Yes. Since these are meant to go over the insert itself colors typically aren't added so that it doesn't darken the insert when lit up. Whitewater has yellow inserts so once you put the decal down it should look correct. Now if you are talking about paint that surrounds the boat then that won't be reproduced in any decal set.
Sometimes you will find the way a playfield was screened will determine what portion of the insert was covered with ink. Sometimes alignment is off from one playfield to another and on some playfields the entire insert is not exposed allowing light to shine through. Here is where insert decals fail miserably; they won't fit perfectly from one playfield to another.
How bad was your playfield in the beginning? Sometimes its much easier to just do spot touchups with acrylic or enamel paint than to remove all of the art and replace with a decal. IMHO the only way to fix significant wear is to take the playfield out of the game and send it off for restoration. Spot wear you can do yourself but depending on how nice you want the end result to be will determine if you need to get a professional to fix the issues.
Reproduction playfields were made for Whitewater (with some issues though) so if you really wanted to you could buy one and swap it in. You could also find an original and send it off for restoration and then swap that in once it comes back. The advantage to an original is the holes are already drilled properly so its easier to swap back in. All of these suggestions are for a pinball that you will never sell, you will find it very hard to recoup any of that money spent.