Is there a way to set up Tbird to automatically archive messages over X days old, or do I have to select individual messages to archive??

The latter. Thunderbird does not automatically archive messages. Also see https://support.mozilla.org/kb/archived-messages

How often or when should archive messages??

That's primarily up to you.

My main email folder is over 3K messages now. Is mere size a problem? Is it a performance issue??

With 3k messages, I'd say neither size nor performance should be an issue.

However, if your 'main email folder' means your Inbox, this is a different story. Inbox is most susceptible for corruption, as the file gets written all the time when receiving a message or moving a message to another folder. Therefore best practice is to keep Inbox as tidy as possible.

I asked because Quickfilter searches seem pretty slow for a folder of 3.5k messages. This was the reason to ask if the folder was too large.

Does Quickfilter use an index? Or is it searching the full text of each email serially for a text string in the email body??

thx, Mark

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Does Quickfilter use an index? Or is it searching the full text of each email serially for a text string in the email body??

That depends entirely on which filter criteria are selected. Body by implication requires a full search. Fields that appear in the user interface list (sender, recipients Subject, attachment Stared unread etc) are in a an index that is used to populate the user interface and will by virtue be faster.