There's usually no good reason to do absolute pathing unless you're doing super complicated stuff. A good example is if the file you're including with #include_function is in turn also using #include_function.
To demonstrate why it would be confusing and absolute pathing would be better, let's take a look at this set up.
MyFolder
|
|---lib
| |---functions.txt
| |---morefunctions.txt
|
|---enemies
| |---enmyFairy1.txt
| |---enmyFairy2.txt
| |---bossRumia.txt
|
|---stage.txt
Ignore the fact that there's obviously not enough stuff to make a good stage. Let's just take a look at what could go wrong with relative path naming.
In functions.txt, let's say that there is a line that says to include morefunctions.txt for whatever reason. With absolute paths, it's obviously what you would put: #include_function "script\MyFolder\lib\morefunctions.txt". However, what would you put if you wanted to use relative paths? Contrary to what you might expect, putting #include_function ".\morefunctions.txt" will not work. This is because when you include functions.txt in one of the enemy scripts, the relative path inside functions.txt makes it relative to the script that is including it, in which case Danmakufu will interpret the ".\morefunctions.txt" as "script\MyFolder\enemies\morefunctions.txt" and not find anything.
To fix that, we'd instead put #include_function ".\..\lib\morefunctions.txt" in functions.txt instead and when we include functions.txt into any of the enemies, it'll work perfectly fine. But then what if you want to include functions.txt into the stage? With the relative file path as it is now, when you call #include_function ".\lib\functions.txt" in the stage, it will in turn call ".\..\lib\morefunctions.txt" which will be interpreted as "script\lib\morefunctions.txt" and not be found.
As you can see, the only way to fix this would be for absolute file paths or a restructuring of your folders. Since organization is fairly important to making a big game, restructuring the folders may not be the best solution and absolute file paths would be the only way.