Under System Preferences > Users & Groups > Login Items, I have a number of applications that are set to launch on system startup.
Some of these, despite being marked to "Hide" on startup, insist on showing their application windows. I have to manually close them.
Edit: At first, we thought that the reason may be that some of them were also set to Open at Login in the Dock Right-Click Menu options (as speculated in the comments below) – but that can't be the reason.
For example, I've just added the mapped network drive
DL below to mount on boot. Despite having checked the box Hide, the folder displays on startup.