That is, is God a deceiver if the omphalos hypothesis is right? I don’t think so, for the following reasons.
Firstly, the universe only has an “apparently old” age in the sense that, when interpreted through a grid which inductively extrapolates backwards from the present, based on current period processes, we can mathematically estimate how long the processes have been running. But it is not as if the rocks have flaming messages from God (a la Douglas Adams) written on them telling us the time and date of their creation. This means that any age they appear to have is based on our inductive reasoning being applied to the objects of nature, not because the objects of nature themselves, or God on them, “tell” us their age.
Secondly, God has never promised that our inductive reasoning will always be correct. As well, we know that our inductive reasoning can often be (and has been) incorrect.
Thirdly, a deception is a falsehood communicated by an intelligent agent. But our inductive conclusions are not propositions communicated to us by God.
Fourthly, if God actually has told us how old the universe is, it is obviously wrongheaded to say that he has deceived us.
Thus I can’t see how the objection sticks. This is not to say that the hypothesis is true: if God has actually not told us the age of the earth (i.e., if non-“literal” interpretations of Genesis are exegetically correct, or if there is no divine revelation at all, or if there is no God to reveal anything), then there is probably no reason to disagree with our inductive extrapolations from current periodic processes. The truth of the hypothesis must be established apart from rebutting the above objection.
(The other objection to the omphalos hypothesis mentioned at wikipedia, that it is unfalsifiable, also fails: if it is established based on it being divine revelation, falsifying its claim to be divinely revealed would remove any reason to believe in a young earth, unless inductive reasoning could separately tell us that the earth was young. So it is falsifiable rationally and theologically, though not through empirical induction from the very things that it says cannot tell us the age of the earth.)