I've had it both ways: With water fills on deck and with them on the top of the tanks beneath the saloon sole. I preferred the on-deck fill.

A few things I was not so fond of with the saloon fills:

1) When I was cruising we didn't have room to stow a large/long hose, so that mean the marina's hose (yuck) was dragged through the accomodations. Yuck.

2) Often, with two people, it's nice to split up tasks while on the fuel dock (to save time if people are waiting especially). Sometimes the hoses don't have shutoffs on the end (and maybe don't even have threads for such), and so there you are in the saloon hoping the other person (who had to now be helping you) would hear you yell out "okay, shut it off" If there was a shut off on the end, you're just hoping it doesn't somehow get dislodged as you thread the hose through the accommodations.

3) When jerry-jugging water, you have to either hump the jugs down the companionway, or carry a siphon hose and deploy it.

In contrast, with the deck fill, you can just pop the hose end in, turn it on, and go about your other business. Jerry jugs are already on deck, and a bit of slopping is no biggie.

I suppose if you have a water maker, then maybe it's nicer to have the (or at least a) tank fills belowdecks (?)

All a matter of preference, of course, but sometimes you don't think of the disadvantages of a new way until you use it (in my case, the saloon fills).