"Lacuna" is a Latin word that means, "hole." It's actually a diminutive of the word "lacus," which refers to a standing body of water, like a lake. In modern language, "lacuna" is used to refer to a gap in something, though it has various more specific meanings in different contexts.
It's not hard to see how this one fits in. The Lacuna procedure essentially leaves a huge gap in someone's memory. In fact, the term "lacunar amnesia" refers to the condition in which someone loses memory of a particular thing or event, so there's even precedence for the use of the word in modern psychology.
Maybe none of this comes as a surprise to you, but if you happen to have Eternal Sunshine with you, you should go to about 1:19:50 and look at the van passenger door. If you do, you'll see that the "C" in "Lacuna" is missing. This not only means that the name mirrors what it means (pretty meta, right?).
In the end, of course, the point is that "lacuna" refers to something that is missing. Although the patients like to think that they're erasing bad memories, it's still not as if these memories never happened. They've left their traces—and now something is actively missing.