"Does .xls file location matter in order to open and access data from the the file in matlab?"
No. Matlab can access files (not just xls) anywhere on your disk.
As for your question. Always use absolute paths instead of relying on the current folder. Despite what you say, if there are excel fles in D:\ and dir doesn't return anything with the syntax you use, then your current folder is not D:. You can check your current folder with:
pwd
But if you use absolute path, it doesn't matter what your current folder is. You'll always been checking the folder you meant:
folder = 'D:';
filelist = dir(fullfile(folder, '*.xls'));
numfiles = numel(filelist)
If dir still finds nothing, then there are no xls files in that folder (perhaps, they're xlsx files).
