They are not where they should be in the span, at least following UK guidance (the USA has a different figure for distance from end-support as 3*depth, not 0.25*span), but they have been like that since it was rewired in the 90s. But the beams are big and the holes, even if made larger, are a lot less than the max allowed.
My feeling is the least-worst option is opening one hole enough for the additional cable, but going to look at just how wide it would be needed to get the various T&E through without drama (can try-drill some scrap wood to see).