Which "word count" do you pay attention to? I've heard some parties say word count = 250 x pages, in which case white space could be a pretty big deal - but if you care about the actual number of words in the ms, seems like it wouldn't matter. Which is, I think, what you said here?
This is one of those things that has been made into a bigger issue than it actually is. Yes, we need to know word count. And yes, there are different methods of counting words. But as long as your query letter indicates which method you use, you're probably not running afoul of any rules. (Check the guidelines first, of course. If a publisher wants you to use a certain counting method, they'll say so in the guidelines.)
Let's look at the differences between the different counting methods. This is an issue of typesetting, a production issue. Think of it this way: the physical book is a container for your story. The container has some small degree of flexibility -- it's a rubber wineskin, not a plastic milk jug. But there will still be a point where a story might not fit the container.
Here's a very simplified look at print production decisions we have to make for each book. We need to select:
Trim Size. This is the measure of the finished page. In America, we measure it in inches. A typical trade paperback is 5 1/2" by 8 1/4", more or less.
Signatures. Most presses can print 32 pages in one pass. These are known as signatures, and for the sake of economy, most books are printed in signature sets, or multiples of 32 pages. (That includes front and back matter.)
Margins. Most books (other than the covers) don't require bleeds (printing to the edge of the page) but allow margins. The size of the margin can vary.
Leading. This is the amount of space between lines of text.
Typeface, or Font. The amount of text on a page can vary a lot depending on the design of the font. Garamond, for example, is denser than Times New Roman, though they look fairly similar. Point (the size of the type) can also be jiggled to get more or less text on a page.
And I could go on, but this gives you a glimpse at some of the major decisions which must be made for each print book that can affect the size of the container for your story juice.
To make things easier and more economical on the production end, we sometimes specify that we want a story of a particular length. We know that we can fit a story that long into a physical book of a particular size. So that gives rise to guidelines for word count. We know, for example, that we can fit a 50,000 word story into a mass market paperback with six signatures and such-and such margins, font, leading, etc. We know we can wiggle that for a slightly longer or shorter story, but wiggle it too much and we have to start changing the shape of the container.
There are two schools of thought regarding word count. One takes white space into account, and the other doesn't. Neither method is precise. But neither method needs to be precise, because all we really want is to make sure the manuscript can be set into a somewhat flexible container of a certain size.
If the guidelines don't specify which word count method to use (and they probably won't), then you can indicate which method you've used in your query letter. For example, if I read,
My Awesome Novel is approximately 80,000 words,
I will assume you're using the pages x 250 method. The word approximately and the round number tells me so. If you write,
My Dazzling Novella is 26,344 words,
I will assume you're using computer word count. In either case, I now have an idea of which container your book might fit into. And that's really the relevant information for me.