What you do by adding the check is preventing the notice from occuring in your log file.
PHP will kind of do the same, in case a variable is not set there is nothing it can do but because it is not checked in code and handled properly it throws the 'undefined notice' in your logfile and it simply continues the code ignoring the undefined variable simply because it is not there in the specific scenario.
The first part is correct, you can see that a function is called using: $item["fk_i_category_id"]
It is the whole part here that return a category id (or not) in case it is 'missing' (not set) it means that the array variable $item is either missing the specific field fk_i_category_id or simply missing completely.
So you check on $item["fk_i_category_id"] resulting in; if( isset($item["fk_i_category_id"]) ) {
If it is NOT set that part of code related to the processing of $item["fk_i_category_id"] gets skipped resulting in a clean log file and for your code there is no change in how it worked before adding that check. If there is an issue caused earlier that was already there it will still be there. You only prevented the undefined notice by handling the scenario of a missing variable here correctly.
So, with regard to the 'cause', the $item["fk_i_category_id"] not being set most likely means that the $item array is not set which would explain the other three notices related to this function.
Meaning, this function got called without $item being properly populated with it's array values, meaning earlier in code there is a scenario where this function gets called while $item is/was not set which can be due to a code architecture ie. the first time it is not yet ready for handling but after the first loop it is...... or something else. The cause is no so important if the whole system does its work but it could be done better probably preventing the scenario from happening but this is how it is at the moment and best thing to do is 'trap' those scenario's with isset (or another check for '' as well) so PHP is satisfied with the syntax and proces flow.