How can I enable counters for folders?

It’s not convenient to see '…'
Please see my screenshot of Thunderbird for better understanding.

I also noticed that emails in folders don’t go to smart inbox folder. You can miss some important stuff this way .

I know what you mean. I saw those three dots only once in eM Client though, and then it reverted to normal and has never reappeared. What version of eM Client are you using?

The smart folder All Inboxes is a combined display of all inboxes. Therefore any folders that are not inboxes will not be included. The Unread folder however, includes all folders.

Thanks for clarifying, Gary! I have a demo right now, it might have some limitations. 
Anyway, my dots won’t disappear. 

I seem to remember that the dots indicate there are unread messages in that folder, but the folder is not synced with the sever. I don’t use IMAP for my regular account, so I could be wrong.

Maybe someone can clarify.

That’s may be the case. I work with IMAP only

I see the dots as well with my IMAP accounts. There are no unsynched  messages, however. They come and go. What I believe is happening is that when my phone touches the mail folders, the timestamp, or something, is changing causing eM Client to believe that folder contents have changed, even though they have not. My phone also uses IMAP IDLE. Now, I just ignore the dots and use the numbers in the Smart folders to indicate how many messages I have unread. It would be nice to get rid of them, though.

By the way, just got an email to one of my folders. Still, nothing is shown in my Unread folder.

eM Client only updates the message status of folders other than inbox when it synchs, and not through IMAP IDLE. So, if you have server side rules that redirect email to other folders, those messages don’t appear in the unread folder. The work around is to configure the messages in those folders to be available offline. They then synch automatically. It would be nice to be able to configure other folders to update through IMAP IDLE. Aqua Mail on Android allows this, and it is useful for those who use server side rules.