When you say regular 4 player rules with an empty seat -- do you mean I don't deal north's hand at all? So a full wall but 3 players?
Sure, why not? It gives each player a possible 6 extra turns to try for that elusive yakuman.
And as far as I know, in the words of Tom Sloper,
There are no mahjong police coming to arrest you for doing it that way.
Have Fun!
Note: The empty seat doesn't necessarily have to be north. It changes as the seats rotate.
If you need "official" stuff, check out sloperama.com
FAQ 13C. Q: "I play Japanese Riichi mah-jongg, and need to know the rules for 3 players."
Remove the suit of Craks, except the 1s, 5s, and 9s. There is no North player (deal only to the other three). Deal always passes to the winner. It's always the East round.
You can read about another way to play 3-player at
http://www.japanese-mahjong.com/3pmjintro.html.
This site seems to be more detailed.
The tiles that are used in the three player game are:
1-9 of Dots (Pinzu) = 9 x 4 tiles = 36 tiles.
1-9 of Bamboos (Souzu) = 9 x 4 tiles = 36 tiles.
1 & 9 only of Characters (Manzu) = 2 x 4 tiles = 8 tiles.
4 Winds (Ton, Nan, Sha, Pei) = 4 x 4 tiles = 16 tiles.
3 Dragons (Haku, Hatsu, Chun) = 3 x 4 tiles = 12 tiles.
Total = 108 tiles
Note: There are no 5-cracks mentioned here
As Scott Miller states in his book, There are many variants for three players, in part because three-player is in itself a modification of standard four-player rules.