For the short answer, see 1 Kings 22:20-23 and Yechezkel 14:9 regarding the use of what, at very least, we would usually identify as deception by God.
Your question, as formulated, relies heavily on the idea that the Biblical stories transpired literally as described while the physical/material evidences (as represented by contemporary academic beliefs) are, as it were, falsified. In much of the Orthodox world, however, it is believed that such evidence provides some justification to interpret these passages non-literally. Regarding a seven-day creation, I would not be surprised if most on a site such as this did not accept the story literally as it is found in the text. The question of deception is even more acute in this case because there is a presumption that we are to interpret the text literally (see how the Meforshim approach אֵין מִקְרָא יוֹצֵא מִידֵי פְּשׁוּטוֹ) and are only permitted to abandon the literal meaning upon finding evidence that the narrative is counter-factual (see Emunos v’Deos 7:2). God tells us what happens in the Torah and it is only through external information unknown for centuries that we are able to tell it wasn't meant literally (according to this approach).
Regarding the notion that the Earth was created to appear old, this is deceptive only when one doesn't think things through. While the Torah obviously provides no information as to how old the earth appeared when it was created fully formed (see Rosh Hashannah 11a) the presence of countless features such as trees would give the impression of more time having transpired than the six-days of creation. Although it would be a sound inference to believe the Garden was older, such inductive reasoning would have to be revised when presented with more information (such as the testimony of the Creator).
Regarding the Israelite's sojourn in the desert, any academic assessment of the historicity of the account will begin with the presumption that the miraculous elements are embellishments as a matter of methodology. That the B'nei Yisrael were fed a supernatural food with a supernatural shelf life (Ex. 16) or that their shoes and clothing did not wear out (Dt. 8:4) means that much of the material culture that we would expect to find as evidence was never produced in the first place, not that it was somehow deceptively concealed.
Just because there is a conflict doesn't mean there is a contradiction. Two of the examples you cited are real conflicts between the Torah narrative and academic science but, at least provided one has reason to believe the Torah account, they do not falsify them. The idea that God could utilize deception is a theologically challenging one but there is some precedent suggesting this to be the case but it is not clear that your examples are the best available ones to probe this question.