If they weren't, they'd desync from the other servers.
Plus, there are upsides to this too. Retainers being back. Airships being back. Levequests accumulating. It's not like any other downtime has been different.
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Our FC got hit by this too: 3 Garlic Jesters, 2 Eggplant Knights, and 3 Krakka Roots. Nothing as valuable as what others are reporting, but still stuff we put effort into. Would be nice if we could get the seeds back or something.
It's been this way since FFXI days - garden timers continue to click over even during server downtime, so any wise FFXI gardener knew not have anything growing when servers went down for maintenance, and it's the same here in FFXIV as well. As others have said, the server downtime was planned and announced a month ago, giving you plenty of time to compensate by clearing out your gardens accordingly before the servers went down.
SE does not owe you anything, as they are fully entitled to take the servers down for maintenance at any time for any reason without any compensation to you for any in-game material loss you may have suffered - it's in the Terms of Service you electronically signed when you first created your account.
Take it as a learning experience, in future when SE announces long server downtimes (such as the upcoming three day downtime for Stormblood's release), you'll know now not to have anything growing in your garden when they take the servers down and prepare for it accordingly, instead of just taking everything for granted. Live and learn and all that.