In terms of technical performance impacts, one could argue that using a single Globals instance is actually more efficient since any libraries are loaded only once instead of multiple times. However the question about usage of multiple files really depends. Multiple physical lua files can be loaded using the same Globals, or a single file can be loaded using the Globals instance, either way the Globals table contains the same amount of data in the end regardless of whether it was loaded from multiple files or not. If you use multiple Globals for each file this is not the case.
Questions like this really depend on what the intended goals are that you wish to use lua for. Using a single Globals instance will use RAM more efficiently, but besides that will not really give any performance increase. Loading multiple files versus a single file may take slightly longer, as the time to open and close the file handles, but this is such a micro optimization it seriously isn't worth the hassle it requires to write all the code in a single file, not to mention how hard it'd be to organize it efficiently.
There are a few advantages to using multiple Globals as well however, each Globals instance has it's own global storage, so changing something, like overloading operators on an objects metatable or overriding functions don't carry over to other instances. If this isn't a problem for you, then my suggestion may be to write the code in multiple files, and load them all with a single Globals instance. However if you do this be careful to structure all your files properly, if you use the global scope a lot you may find that keeping track of object names becomes difficult and is prone to accidentally modifying values from other files by naming them the same. To avoid this each file can define all of its functionality in it's own table, and then these Tables work as individual modules, where you can select features based on the tables, almost like choosing from a specific file.
In the end it really doesn't make much of a difference, but depending on which you choose you may need to take care to ensure good organization of the code.
Using multiple Globals takes more RAM, but can allow each file to have their own custom libraries without affecting others, but comes at the cost of requiring more structural management from the Java end of your software to keep all the files organized.
Using a single Globals takes less RAM, but all files share the same global scope, making customized versions of libraries more difficult and requires more structural organization from the Lua end of the software to prevent names and other functionality from conflicting.
If you intend other users to use your Lua API to add-on to your software through an addon system for example, you may wish to use multiple instance of Globals, because requiring the user creating addons to be the one responsible for ensuring they're code won't conflict with other addons is not only dangerous but also a burden that doesn't need to exist. An inexperienced user comes along trying to make an addon, doesn't organize it properly, and may mess up parts of the software or software addons.