You are joining a startup. To you it's just a great opportunity at a job that seemed interesting to you. To the founder, it's his life. At 2:30am you might be leaving the bar thinking about whether to call an Uber or a Lyft. Your founders are probably awake thinking about how they're going to get that new feature out the door.
I started my own startup a little over 2 years ago. It's pretty normal every night between 2 and 5am for one of the three founders to send a message to another about something they're freaking out about.
He's not thinking "Oh it's 3am, I shouldn't email my employee this late". He's thinking "There's something on my mind about my company and I need to get it off my chest".
If you start your own company and get a few employees it makes a lot more sense VERY quickly.
Don't worry, he/she's just very invested.