Can a location or item be locked down so that transactions against it are prevented during Stock Counts?

There is no way to lock down an item or location so that transactions are prevented against it during Stock Counts.   The program does have a safeguard built in to prevent counting errors due to active transactions.  As a safeguard, the Stock Counts screen will "throw out" the count on any item that has had a transaction against since the creation of the Stock Count. It will then report that it did not update the count for that item.  

Your overall strategy for stock counts should be to freeze activity for all items on an active stock count and perform the count in as timely a manner as possible.