Q:

startup etiquette: employee and supervisor meeting without me

I am the cofounder / CTO of a very small startup, ~4 people.  We recently had to let go 2 people for differing reasons.  As a result, we moved one engineer from working mostly on metrics to work on our web server.  That employee is a direct report to me but is personal friends with our CEO, as am I; we're a small startup of mostly friends.  
We have been discussing some technology changes in the wake of the company changes, and have had several meetings in the past week or so about this.  
Last Saturday, the engineer and our CEO had brunch.  They did not tell me that they were doing this ahead of time, and they discussed a number of work items.  My employee told me last night that they had met, as well as which items they discussed, which I appreciate.  When I asked our CEO afterwards what they discussed, he said that it was "just brunch."  I said that the engineer had mentioned that they discussed a few work items and we then reviewed those. 
We're a small startup, and I don't begrudge anybody their social time with anybody else, but am I wrong for feeling that they should have let me know that they were meeting, particularly if they were planning to discuss work items that I had a vote in?  I appreciate that my employee let me know afterwards, but I also am a little wary that I was not included or notified except belatedly. 

A:

If no malice is intended, no ill will exists and no foul play is in the works, then I suggest that you take things at face value and go with the flow. 
Take the attitude as the CTO, anything that has to do with technology and that affects the firm - that anything has to go through your review and approval.  As long as the CEO and your report are clear that they can't abrogate your prerogatives and bypass your responsibilities and flout your authority, they can do anything they want including having breakfast, lunch and dinner with each other and go to the movies with each other every day of the week for all you care. 
If you feel insecure with your authority in the firm, it's a problem.  If the company's top management and staff make technological decisions, bypassing their own CTO, then it's a bigger problem because it affects the functioning of the company as a whole.  
I trust that you were not put into the CTO position so that they could then bypass you.  It would make no sense if that happened and the angel investors and the VCs would be up in arms about it.  Especially if you are expected to step in as the top dog if the CEO were to get run over by a truck.  

A:

We're a small startup, and I don't begrudge anybody their social time
  with anybody else, but am I wrong for feeling that they should have
  let me know that they were meeting, particularly if they were planning
  to discuss work items that I had a vote in? 

Feelings are feelings - they aren't right or wrong.  But you may need to work on trust here. 
Startups need everyone to be working hard on lots of things at the same time.  You want your team to get together often, and if work items are discussed - all the better. 
I've worked in several startups, and as a CTO you simply cannot be present at every discussion.  Hopefully you hire people you can trust to discuss things without your presence - otherwise your venture can never scale. 
Train your people to understand what conversations and decisions require your approval, and which do not.  Hopefully, you have far more of the latter - saving your time for the important discussions and decisions that really matter. 
As your venture proceeds, your CEO will have many conversations with many people and you will not be present for all of them.  If you cannot trust your CEO in that regard, your startup may be in danger. 

I appreciate that my employee let me know afterwards, but I also am a
  little wary that I was not included or notified except belatedly. 

Unless they were deciding company direction without involving you, it's hard to see that discussing "work items" over brunch is something that should bother you.  Has something occurred that makes you so suspicious?  Hopefully not. 
I'm assuming that during this brunch nothing major was decided that you can't undo.  
Trust that your CEO knows how to tell when you must be involved in food and talk going forward.