My current company used to have logos on literally every document they used. Even if they wanted to send an internal memo, they used the logo!
I removed this system, mainly because of these reasons:
1. I find it of no logical use for all internal documents.
2. They take up quite a bit of file space, especially if they are high resolution logos.
3. They use pretty good amount of printer cartridge ink when printing. (If you want to print a 4 line page on a color printer, it takes atleast twice the amount of time to print if the logo is in there!)
The only place I have maintained the logos are on the Quality Policy and on the Quality Manual, both of which are many a times required to be submitted for tender purposes and if suppliers and clients ask for them. On the rest, I have the company's full name typed in the top right hand corner of the header.
Seems fair to me this way!
Ciao.