I suspect the problem isn't in the if condition - but in the statement that follows. I would start by reformatting the code like this:
String description = getConfig().getString("core.commands." + cmd + ".description");
if (!description.isEmpty())
{
    getCommand(cmd).setDescription(description);
}
else
{
    getLogger().warning("NO description assigned to: " + cmd);
}
(I've removed the description = null; statement as it's almost certainly unnecessary.)
With that change, you'll be able to tell more about what's throwing the exception. You can go further:
String description = getConfig().getString("core.commands." + cmd + ".description");
if (!description.isEmpty())
{
    Command command = getCommand(cmd); // Or whatever type it is
    command.setDescription(description);
}
else
{
    getLogger().warning("NO description assigned to: " + cmd);
}
Aside from anything else, when you now step through the code in a debugger (assuming that's even feasible) you'll be able to tell whether command is null (which I suspect it is). If you can't use a debugger, you could at least add logging.
(Others have already suggested checking whether description is null, but it sounds like that isn't the problem, which is why I've suggested that the problem could be within the body of the if statement.)