[[ $foo -eq "Y" ]]

[[ $foo = "Y" ]]

Shells have two sets of comparison operators: for integers (-eq, -gt, ...) and strings (=, >, ...). ShellCheck has noticed that you're using an integer comparison with string data.

If you are in fact comparing integers, double check your parameters. Certain mistakes like $$foo or ${bar}} can introduce non-numeric characters into otherwise numeric arguments.

None.