This is ok to do once in a while, but is not a best practice for long term usage of your memory card. Hudson even comments on this in some of his later videos, after he initially brought up the idea of deleting photos on the card in order to preserve your config files.
When you delete the files on your card, vice formatting, you start to get non-contiguous blocks of free storage space (fragmentation), which is not efficient and can get worse over time. I've also read that it can increase the likelihood of eventually corrupting the card.
Formatting your card basically resets the filesystem to an initial clean state with maximum contiguous free storage space.