Disabling startup items that run on their own
Day One seems to store the login item in /var/db/launchd.db/com.apple.launchd.peruser.501/overrides.plist:

$ /usr/libexec/PlistBuddy -c 'Print _com.apple.SMLoginItemBookmarks:com.dayoneapp.dayone-agent' /var/db/launchd.db/com.apple.launchd.peruser.501/overrides.plist
book 0(UserslaurTorrents
                        Day One.apContentsLibrary
LoginItemsDay One Reminders.app $4HXh?kld ????$A????H???A?1M?$5DF7A03E-A7FB-3E80-B61D-F10CD8BF7B5D?/?0c75ae904b0f99cb3a794e7360629c822a0f4a14;00000000;0000000000000020;com.apple.app-sandbox.read-write;00000001;01000002;0000000000641712;/users/lauri/torrents/day one.app/contents/library/loginitems/day one reminders.app??????D|@l 0 ? ? ? ?  0 &lt;???????D


Changing this to true in that same file disabled it:

&lt;key&gt;com.dayoneapp.dayone-agent&lt;/key&gt;
&lt;dict&gt;
    &lt;key&gt;Disabled&lt;/key&gt;
    &lt;false/&gt;
&lt;/dict&gt;