It's more to do with certain services (SatoshiDice) sending very small, useless transactions through the network (SatoshiDice is a gambling service, they send a small transaction to tell you you lost). All those small transactions put a burden on the network.
Regarding the CP URL, it was actually several hundreds of links in a large FAQ, and I don't think this changes anything regarding encoding data in the block chain.
From what I read on bitcointalk I believe this applies to miners too (if they use bitcoind). However it would be possible to run a mining pool which would accept small txs with no fee, and clients would still accept them as valid blocks.
Regarding the CP URL, it was actually several hundreds of links in a large FAQ, and I don't think this changes anything regarding encoding data in the block chain.