Is it ever worth it to purchase Shrines?

Usually I just invest in more permanent defenses. Is it ever worth it to purchase Shrines?

Not really. Shrines are still godawful expensive even after the update. Their utility is great as a panic button of sorts, but you're better off in the long run spending your mana on real defenses.

Well there are several battle amulets for building and using shrines so to maximise the potential xp per battle they can be useful. Other than that I've never really needed one to complete a level.

Yes. When the strength of monsters exceeds anything you can hit them with in your arsenal. For example, if I summon 5000 monsters in one wave with an HP of over 10 trillion, I might be in trouble. However, if I have 8 or so shrines capable of targeting a large portion of the group, I can drop the highest 8 gems that I can afford in there. The initial wave coming out of a lightning shrine reduces monster health by a percent of current health.

If the reduction is 50%, after 10 shrine uses, those 10,000,000,000,000 hp points will be a mere 9,765,625,000. Certainly more manageable. As this is the case, provided that such a large wave doesn't crash your computer, you can really kill just about anything.