The latter. The reason this happens is because the Desktop (unlike any other folder) is constantly being refreshed. So the more items on it, the harder the processor has to work to constantly refresh/re-index the contents.
I didn't read the article (since I've been preaching the "clean your dang desktop!" mantra for years now), but here's my other simple tips to keep your Mac humming along for years on end.
1. Keep a lot of free space on the hard drive available at all times. "A lot" is a phrase everyone has a different interpretation of, but I say a dead minimum of 12-20GB (depending on the amount of RAM you have, virtual RAM space in reserve has to at least triple your actual RAM), and a lot more would be a lot better. Mac OS X just needs a LOT of "elbow room" to do it's thing, particularly if you're working with media apps.
Basically, if you have less than 10% of your drive available, it's time to either do some spring cleaning, move the media files to their own drive or think about getting a bigger HD. You're not asking for trouble yet, but you will be if you let that drive get much below 10% free space.
2. DO REGULAR BACKUPS. This should actually be point #1 but I'm lazy.
3. Every so often (not all the time, just periodically) run a quality utility tool like OnyX (**NOT** MacCleanse!!) on your system.
4. (Optional) This last one is just my personal practice, I backup to both a Time Machine drive AND I use a clone program (
SuperDuper or
Carbon Copy Cloner) to make a bootable clone on a different drive. Copies or really irreplaceable stuff also gets periodically backed up off-site (for most people, there's not really much stuff that is genuinely irreplaceable other than photos or financial/legal records).
5. Because I have a bootable clone on hand, about once a year I like to do a "nuke and pave" on my boot drive, by which I mean I start up from my freshly-made clone drive and ERASE (zero out) my boot drive, then restore back from the clone. Macs don't generally need "defragging" or "optimizing" but once a year seems to me to be a good idea to me. Makes a minor difference in speed but noticeable -- at least for a while.