First Registrations are usually lengthy and complicated. I've never seen a case where it took 9 years to get the first queries from the land registry but that doesnt mean it can't happen.
Typically in a First Registration it could take a couple of years before one would hear from the PRAI or land registry. It would then be quite common for the queries to take the form of a long letter with two or three pages of questions. One of the most common queries is the names of all adjoining owners. They may be served with a notice from the PRAI asking if they object to the application.
It could mean that the solicitor delayed in lodging the application or it could mean that this particular case became unusually delayed or it could mean that there was more work for the solicitor before they could lodge so they had to do that first before lodging. If it is important to know why it took so long then it is easy enough to find out the date of lodging for registration by the solicitor- or just ask them why it took so long. They should be upfront if the fault was at their end. At the end of the day the important thing now is to perfect your mother's title.
As for cost- if your mother was already billed for the first registrationa and paid it, she shouldn't have to pay again. She may have to pay any additional outlays such as search fees, if the land registry have requested these and she hasnt already been billed for them.
As for whether the queries in bold are more important, I just don't know off hand, although I do these all the time!