The answer to this is yes. Unless a ship is declared completely no smoking there will always be policies in place to cater for both smokers and non smokers.
The situation also changes dependent on locations. Ships working on European business will often follow European land law and not allow any smoking inside public areas, which include the bars and clubs. Most other ships will at least make some public areas completely no smoking.
Most cruise ships have stopped smoking within cabins, suites and staterooms, and many have also included hefty fines for passengers who smoke inside against the rules. A fine of over £200 is not uncommon, which the cruise companies state as cleaning charges to remove all traces of the smoking offence in the room. An exclusion to this cabin rule is some cruise ships will allow smoking on balconies
A rule of thumb for smokers is to follow the ashtrays, cruise staff, as part of their bar and general duties will place and change ashtrays. If ashtrays have been placed in an area, then it is obviously a smoking area. Also watch out for wall mounted ashtrays on the open decks, these are often placed in areas where it can get windy and are designed in such a way, that the ash does not become an issue for other passengers. These do however, need to be checked when using, as non smoking passengers can often use them for depositing tissues and napkins which becomes a small inconvienice and hazard.
The best policy for a smoker is to check before you book, and then once on board, check where the smoking areas are. Staff will happily show you.