My solution was to specify my custom shares and stuff by utilizing smb-local.conf, which takes precedence over smb.conf. I was not able to solve it in any way when using smb.conf, unfortunately.
I don’t recognise the problem. I have never had anything other than the home directory and USB disks show up as shares.
OK, thanks. Was there something you put into smb-local.conf to fix it (like veto files = /boot/ ?
It just seems strange because I had “boot” showing up on a clean install (before creating a smb-local.conf file). And I never had to specify a veto record on my other boxes.
Same here, for previous installations! My other installation with SMB share (a Pi2) looks like this, where “Pi” is a folder I created in the home directory.
But just today I booted up a brand new Pi3 on the December release. I then installed Samba Server from the OSMC store. I was going ahead to setup another “Pi” directory to hold my scripts, when I noticed this unusual “boot” directory. I thought I’d search, and found this thread where others had similar observation. Not a big deal either way, but I am curious.
Unfortunately, vetoing the boot folder did not work for me, so I went the smb-local.conf route and haven’t had a problem since.
Thanks! On my OSMC the “boot” share is created by /etc/udisks-glue.conf into /var/lib/samba/usershares/ so i created an empty directory “boot” there 
This works too:
smb-local.conf:
### hide /boot and /EFI
[boot]
access based share enum = Yes
[EFI]
access based share enum = Yes