I know that I have not much free space on my data hard drives: free space is space wasted there. I don’t need being notified about it every minute or two.
Unfortunetely, both buttons on pop-up don’t do anything. It doesn’t matter if I click “Ignore”, as the pop-up gets back anyway to nag me. The option of Examining it out, doesn’t do anything as well. It doesn’t matter what I click, the pop-up gets back anyway.
Since this is quite distracting and irritating, I’ve tried to turn it off in overall notification settings in Gnome settings. There is “Do not disturb” mode, but turning it on, doesn’t change behaviour of the pop-up.
Clicking on pop-up opens up Baobab, but Baobab itself isn’t included on list of applications suitable of turning on or off the notifications.
When I add my disks on Baobab’s ignored list, that doesn’t solve the pop-up behaviour as well.
What can I do to neutralize it?
Urgent notifications are exempt from the do not disturb setting because they are critical: power, storage, and other hardware related issues that need your attention now , or might result in loss of data or functionality.
– Emmanuele Bassi, GNOME Developer
Having said that, you can disable notifications under Settings > Apps > Disks.
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Well, that didn’t happen when I had my other disks absent from fstab and I mounted them manually.
Now I’m getting bothered with it consistently.
Take another approach: instead of silencing notifications after a service discovers you are low on space, try to find this checking service and disable it.
Forgot to mention…
However, see @Aragorn’s reply below 
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You appear to be missing the fact that certain filesystems need a certain amount of free space in order to be able to operate.
So it’s not wasted space, but space required for normal filesystem maintenance operations. Your concern should therefore be to free up space by moving needed data to other storage devices and/or by deleting unused/unneeded data.
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I don’t use Baobab (nore Gnome) but found a way to exclude a disk by command line (URI of device path, e.g: file:///dev/...) and URI of a path in a filesystem too (e.g: file:///home for mountpoint of /home). Perhaps both, disk URI and filesystem URI are neccessary. Did you try that?
gsettings set org.gnome.baobab.preferences excluded-uris "['file:///path/to/your/disk', 'file:///another/path']"
Reset all:
gsettings reset org.gnome.baobab.preferences excluded-uris
Certain filesystems need a cetrain amount of free space, sure. But not those I have mounted in my system.
Besides, what I am not missing, is user choices should matter.
If system gives me choice of resolving or ignoring issue with its GUI, when I click “Ignore”, it should, well, ignore it, at least to the time of next reboot. What’s the point of informing the system of my intention, if it’s going to be discarded anyway by amnesiac that can’t remember what I’ve decided minute ago?
Right now it seems “Ignore” button seems not performing its function.
Pardon my cynicism, but then GNOME is not the right user interface for you. Its developers do not believe that users would be capable of having any other preferences than they themselves have.
GNOME is one of those projects where they protect the user’s freedom by taking it away from him/her/them.
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They then keep it in a safe place where no one can get at it.
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I don’t think one can say they have no freedom - Gnome is an elaborate educated choice - a work style - if you don’t like it - don’t flame it - just use something else.
Gnome users have the freedom to work focused - zen focus - and they have the freedom to use something else.
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I suggest either turn off monitoring of data drives in baobab preferences, or use dconf-editor GUI or dconf or gsettings to adjust housekeeping settings
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