Yes, in most cases the search results can be set up to show each hotel only once and keep the lowest available price, so your customer does not see the same property listed three or four times. This happens because a single hotel is often sold by more than one supplier, and each one sends it through with its own price and its own way of writing the name and address.
The matching behind this is good but it is not perfect. Large and well known hotels are usually recognised and joined together without any trouble. Smaller guest houses, apartments, newly opened properties and hotels that have recently changed their name are the ones most likely to slip through as two separate entries, because the details coming from each supplier do not line up closely enough to be treated as the same place. So you should expect the odd duplicate rather than none at all.
It is also worth knowing that the cheapest option is not always the one your customer would pick. One supplier may be offering room only while another includes breakfast, and one may be fully refundable while the cheaper one cannot be cancelled at all. For that reason many agencies prefer to show the hotel once with all the room options listed underneath, so the customer can see what they are actually comparing instead of only the lowest number.
Run a few searches in the cities you sell most, see how the results look to you, then let our team know whether you want cheapest only or all options grouped under one hotel, and pass on any duplicates you spot so the matching can be tightened.