It'd be heavily application dependent. With applications I've deployed, it's been irrelevant, as there's absolutely no directory traversal of the application directory going on from within the applications. Some frameworks, particularly Rails, will do auto loading of files within the application and do directory traversal to discover those files, but typical
Dir['**/**'] type affairs skip any "hidden" directories such as .svn and .git.
If, for some reason, your application or framework had need to traverse all files under the application folder and didn't ignore hidden directories, there might be some negligible effect, but it would be so application and situation specific that you'll struggle to seek much advice from a generalized answer.
All that said, if you have no reason to push changes back from deployment to the SVN server and you're using a multi directory rolling style deployment mechanism (that is, you export/check out to a new directory every time then update a symlink or similar) you might as well go over to using export. If you just
svn update within a deployment directory each time, you might want to stick with it for efficiency's sake..