... make a big difference on distribution of iowait load (which, in sum, will be the same of course).
Directory entries are stored in blocks, and they will be read from disk (assuming a disk based file system, if it's memory based, I/O wait will be far, far less) block by block. While using 'ls' means all the blocks for the directory (one for a small directory, more for a large directory) need to be fetched and read, it also means each block will be processed quickly, and once processed, it's not needed again. It's quite likely that the block will remain in the buffer cache the entire time it takes to process it. OTOH, when doing readdir, and processing the file after reading each entry from the directory, there's a probability (which increases the larger the fetched file is) the block will disappear from the cache before the readdir loop is done with it, requiring a second fetch of the same block.
Whether this is actually measurable is a different matter.