Another possibility is that they were custom holes for drain lines down to a sump and/or returns up through a decoration. Either way, they are there and you can use them to your advantage. Get through hole fittings for the hole size and use PVC
standpipes. Have them drain into a sump ( any sump that can handle the volume of water you need to need to have in the system) or use some as a return and just use decorations to hide them. Having them already drilled opens up a lot of possibilities for you. That's a gift you may not realize just yet.