I highly doubt they are going to be ghost towns for the first few months. Wrath of the Lich King is Classic WoW at its peak. All the people I know that dipped their toes in Classic Vanilla er coming back for Wrath of the Lich King. Most of them had zero interest in TBC: Classic. And most of them would prefer a fresh server as they don't have any level 70 characters to move over to WotLK: Classic and they prefer to play with a new wave of people from level 1 instead of paying for a level 68 character boost.
But unless Blizzard walks back on this whole 90-day thing I suspect a lot of potential fresh players will be rather sceptical. There is no real point in having a fresh server if it's going to get a huge influx of character transfers and boosters after the 90-day mark. This is just making things very uncomfortable, as people considering joining a fresh server have no clue what's going to happen to the server once it hits the 90-day mark. That's a lot of time and effort put into a fresh server only to have it all go mayhem after 90-days.
Blizzard will also have a hard time balancing this. How are they going to deal with the number of fresh servers? Only 1x PvP and 1x PvE server in all regions? That sounds like the best idea, considering how easily the servers might end up deserted if they open too many. But the influx of players the first few weeks might be way too high for this to work creating another Vanilla Classic scenario with queues going for 10 hours+ making a lot of players leave the fresh servers before they even got started.