It's an ad because they are advertising the iCloud service to you. It's not just that they say "Your iCloud is running out of free space", it's that they say "Your iCloud is running out of free space, buy more space here!"
That's not an advertisement. That's a critical notification about a service you've chosen to use. It's not any different just because they offered a free trial.
No, I expect it not to try to sell me something at all. If I'm close to my capacity limit, it just means I need to clean some of the crud out.
It's not that they say "Your iCloud is running out of free space." or "Your iCloud is running out of free space, buy more space here!" it's that they say "sign up for iCloud and store your X!". The first two are status updates for a service that's already being used. The last is an ad.
It's an install option for OSX and you can trivially disable it as well. OSX runs just fine without it.