According to preliminary official results, the turnout at the Catalan independence referendum was 42.58%, but Wikipedia also notes that The Catalan government estimated that polling stations representing up to 770,000 electors were closed down by police in raids, which makes it hard to interpret/compare the 42.58% figure; at best it's a lower estimate of what the turnout would have been without those closures. If we subtract those 770,000 from the 5,313,564 registered voters, the turnout among those who were able to vote at all would be 2,262,424/(5,313,564-770,000)*100%=49.8%. But that is a very approximate figure. Are there any official estimates of the turnout considering only those polling places where people were able to vote and ballots were not seized by the police?
Such an estimate would not be reliable, as the requirement for voters to vote at their designated polling station was removed in the last hours before the referendum began. Therefore, polling stations which functioned throughout the entire day would show a disproportionate turnout as they would have gotten additional votes from people who were turned away from their assigned polling stations.
While I am not aware of any such statistics, the only somewhat reliable way of getting such an estimate would be to compile a list of polling stations which functioned regularly throughout the entire day, voters assigned to those polling stations and the percentage of those people who actually did cast a vote. Assuming there was a proper registration of voters (from which one could tell who voted, and which was effective in preventing double votes)—which the comments seem to indicate but which I do not know for sure.
Even under the above assumptions, these figures would still be unreliable as indicators of what participation would have been if the police had not attempted to prevent the referendum. According to news reports, voting was not possible for the first few hours after the polling stations opened, which may have resulted in people not voting. Others might have chosen to stay at home because they did not want to get involved with clashes in the police.