With the housing system currently down, will the items that we gain during questing and such that overflow into our banks still be available or are they lost forever?
Your bank will continue to overflow and when you get back to your room, you will see the overflow amount. Example 125/100 items.
As for plants, time is still passing. During this maintenance your plants will only degrade one 'level' of health. If your plant was healthy the last time you logged in, it will either still be healthy or it will have needs and pests when you log in tomorrow. If your plant had needs and pests the last time you logged in, it will either still have those needs and pests, or it will be wilted. If your plant was wilted the last time you logged in, it will either still be wilted or it will be dead. If your plant was dead the last time you logged in, well, it's still dead. Sorry.
If you want the prize, you have to build the ladder rung by rung. There are no shortcuts.