Does leaving empty PCB holes filled with solder matter?
No, it is not an issue.

In a (huge) quantity production setting you might think about the wasted material (and there's that rumor about the mass fraction of the Saturn V) but for an ordinary prototype it should make no difference.

Should you later decide you wish to put a component lead or wire there, you may need to clean out the hole with flux and desolder braid, or some other method of your choice.