In mongoDB here is the output from Mongoshell. can you please see if this can be converted to laravel/whatever your program syntax is there? Please note exists is used with a prefix $ sign in mongo, that is not there in your code.
> db.multiArr.find();
{ "_id" : ObjectId("5f4d1fd58379a4e3f957641b"), "ID" : "fruit1", "Keys" : [ [ "apple", "carrot", "banana" ] ] }
{ "_id" : ObjectId("5f4d1fd58379a4e3f957641c"), "ID" : "fruit2", "Keys" : [ [ "apple", "orange", "banana" ] ] }
{ "_id" : ObjectId("5f4dc7d6673d93c7e20e48f6"), "ID" : "fruit3", "Keys" : [ "figs", "dates", "apple" ] }
{ "_id" : ObjectId("5f4dc86d673d93c7e20e48f7"), "ID" : "fruit4", "Keys" : [ ] }
{ "_id" : ObjectId("5f4dc99b673d93c7e20e48f8"), "ID" : "fruit5" }
> db.multiArr.find({Keys:{$exists:true,$ne:[]}});
{ "_id" : ObjectId("5f4d1fd58379a4e3f957641b"), "ID" : "fruit1", "Keys" : [ [ "apple", "carrot", "banana" ] ] }
{ "_id" : ObjectId("5f4d1fd58379a4e3f957641c"), "ID" : "fruit2", "Keys" : [ [ "apple", "orange", "banana" ] ] }
{ "_id" : ObjectId("5f4dc7d6673d93c7e20e48f6"), "ID" : "fruit3", "Keys" : [ "figs", "dates", "apple" ] }
>