> Are there any drawbacks to shuffle() other than being "more difficult"?
You won't have the presentation order during analysis, should you need it. And you should not allow for a "back" button, because people were able to re-rotate the pages, if they visited the page again - as long as you do not use `registerVariable()`. That's all, only little things that make the whole thing a bit more vulnerable for non-intended behavior.
> And is it OK to use the same page IDs (e.g. P1, P2, P3) in different questionnaires as the IDs are collected locally
The page IDs are not collected (in the sense of "collected data") at all, so you ca use the same in different questionnaires.
> This isn't something I necessarily need in my data collection is it?
Usually not, but some people make a big fuzz about it (although most of them never actually run analyses on the presentation order).