Is this a good excuse to miss my first day of work?

They might give you a pass if you explain the situation, but I am pretty sure they aren't going to be too happy with the fact that you may need to call in due to surprise workshops. They need to be able to rely on you, and know you are going to be available for your shifts. If you are able to get past this and they still want to keep you, make absolutely sure that you tell them exactly what your scedule is, and the exact shifts they are going to need you for.

Stick to what you told them at the interview. The boss doesn’t remember everything for everyone. 

I am sorry I can not make it on Monday.  I did mention during the interview I can not work Mondays and Thursday. 

Don't lie.  Tell them that you aren't available since you said you weren't available on Mondays.  You might be out of luck on this job - some places only do trainings on certain days.  And maybe this is a good lesson on not waiting until the last minute to do your school work because you should be able to take a few hours away on the day that something is due.

That sounds like a very flimsy excuse. 

Why make up a lie, anyway? Tell him "I told you at my interview I could not work Mondays or Thursdays, and this training is on a Monday. I was hoping I could juggle my schedule to fit it in, but it turns out I can't. Is it possible I could do this another day?"

Will they still hire you? Possibly not. But they wouldn't with the "surprise workshop" excuse either. And unless this job is something you're happy to do for the rest of your life, don't tank your university grades to work there. Do a good job on your essay, and find a better job. The job I had as an undergraduate was happy to work with my class schedule; I'm sure you too can find one that is. 

Lying gives away some of your most valuable possession; your self-integrity. I cannot understand the scheduling issue.

Is the essay due at noon or midnight? Is the server training 4pm-8pm? 

If you cannot do the half shift because of schoolwork, then that is what you tell him. When was the large essay assigned that is a major part of your grade, and why is it on the last day? Excuses in a low paying job are meaningless to them anyway. You either can or cannot be there, and it makes no difference what the reason is. They hire to fill time slots. 

I don't make up stories. If you cannot tell him what is up, you don't deserve the job. If you can't make it, and already said you can't work Mondays and Thursdays, then just stick with that. If class ends on a certain date, tell him that.