Hi,
Regarding iDeal I wouldn't be able to tell you as we didn't develop that payment plugin. You should contact the support of your iDeal payment plugin provider for that question.
For PayPal, indeed the invoice number passed on to PayPal is the order ID and not the order number so that when PayPal notifies HikaShop we can clearly identify the order as the id is always unique. The order number on the other end could happen to not be unique based on how you configure the "order number format" option of the configuration.