Appealing to God’s ‘mysterious ways’ is nothing new. I’m sympathetic to the idea that skeptical theism is just a more dressed up version of appealing to God’s mysterious ways. Whether or not that is the case, I do not think skeptical theism is plausible in its own right. I think skeptical theists admit defeat.
What we see in the world is an abundance of horrific suffering. This isn’t the least bit surprising on naturalism, as I’ve argued in the past (in fact, it seems obvious to me). On classical theism, however, this isn’t what we would predict the universe to look like; we wouldn’t predict horrific suffering.
Skeptical theism comes in and says we shouldn’t expect to see God’s reasons for allowing evil. We can’t say whether theism predicts or doesn’t predict horrific suffering. That’s because, according to some skeptical theists, we have no good reason for thinking that the goods we know of are representative of the goods that there really are.
Some issues with Skeptical Theism
Firstly, at least pragmatically speaking, however, this (i.e. the above) is tantamount to admitting that theism doesn’t predict horrific suffering , and it is equivalent to saying theism doesn’t explain the existence of horrific suffering as well as naturalism (because we know naturalism predicts the data). Rather than coming up with an explanation or theodicy, the skeptical theist throws in the towel. One can only wonder if this is due to fact that most professional philosophers of religion find most theodicies to be implausible. If there were a good theodicy at the moment, one also wonders why any theist would be a skeptical theist. Saying that it is unknown whether (classical) theism predicts the data of evil is (for all intensive purposes) the same as saying that theism fails to predict evil. As such, skeptical theism should not be seen as some sort of sophisticated position. At least theists who give theodicies are trying: skeptical theists quit the game before it even starts. Appealing to mystery or unknown reasons is a strategy that can work with anything, save any hypothesis, and render a hypothesis useless/unfalsifiable; it’s a strike against a hypothesis, and we are still left with naturalism predicting the data of evil.
Secondly, appealing to our cognitive limitations doesn’t really help. On naturalism, there is nothing surprising about human ignorance. It’s arguable that human ignorance is way more expected on naturalism than theism. On theism, God can make creatures with way more knowledge than humans in the actual world. The upshot is that even if theism predicts that we will be ignorant about many of God’s actions, that doesn’t mean we will be ignorant about God’s actions when it comes to suffering. Particularly, there is nothing about theism that predicts us being ignorant about God’s reasons for the horrific suffering of animals . On naturalism, however, there is no God to tell us his reasons for allowing suffering.
Thirdly, skeptical theism is a version of theism, which means it is incredibly less simple than naturalism. The reason is that skeptical theism is an auxiliary hypothesis of theism. In addition, theism is a form of supernaturalism; it’s possible to be a supernaturalist and not a theist. Not to mention, classical theism itself is just one form of theism . Couple that with the fact that skeptical theism doesn’t explain anything, it’s quite easy to see how naturalism comes out on top. Thus, like with many theodicies, the skeptical theist’s move fares no better.
Fourthly, even if we grant that, for all we know, God has morally sufficient reasons to allow horrific suffering, it is also true-and antecedently no less likely– that for all we know, God does not have morally sufficient reasons for allowing horrific suffering. Therefore, we are left right back where we started, which is that suffering is surprising on the hypothesis of classical theism. Not to mention, for all we know God is able to accomplish all she wants without the existence of horrific suffering. Furthermore, for all we know, there are worse evils that are gained by the existence of present evils. Thus, if anything, appealing to unknown reasons makes it antecedently unlikely that God really does have a good reason. 
Thus, even if we grant skeptical theism, nothing changes. In fact, skeptical theism doesn’t even try to explain evil. The skeptical theist throws in the towel. They admit defeat.
 See Null Hypothesis: https://en.wikipedia.org/wiki/Null_hypothesis
 One also wonders why God, if God exists, doesn’t tell us his reasons for allowing horrific evil. Even if we can’t understand his reasons, God could at least assure us, if she exists, that there really are reasons. At minimum, God could always be present and make God’s presence felt to those who are going through horrific suffering.
 One also wonders how skeptical theism is supposed to fit in with Judaism, Christianity, and Islam. In the Bible, Yahweh does tell us his reasons for doing various things, and some of those reasons seem dubious.
 See Michael Tooley: https://plato.stanford.edu/entries/evil/#IndLogEviArgEvi