I actually do prefer having all basic levels unlocked from the start. Since I'd still like to give players a good, consistent reason for collecting bolts (something the first Spyro game didn't really have), what I might do instead is add something that can be activated in each level to obtain something else for collecting all of the level's bolts. Simply rewarding a golden gear, the way Super Mario 64 rewards the player for collecting 100 coins, may be enough.
Hubs will be separated into their own scenes, bridged by portals or other scene transitions. This is to facilitate hubs potentially being very different from one another without overcomplicating level design.
I quite like the space idea, if only for a single flight level. One of the hubs will be based around desolate biomes (icy caverns, a desert, and mountains), and I can't think of a more fitting desolate biome for a flight level than space. So, I've just added that to the design notebook!
Now's a good time to make suggestions like this, because very little is set in stone yet. A lot of things will naturally fall into place as I implement new things and playtest the game myself. After all, I'm simply making the game I want to play and will immediately know when it includes something I don't like. But, some decisions may be far too late to change if they aren't brought up early on. And, level themes certainly fall into that category.