water in bilge of 1999 sailfish..scupper problem?

It could be a number of things, but yes. What's the condition of the hoses? Is it salt water or fresh water (taste it, if need be). Dry the bilge out completely, observe closely. Paper towels placed in key areas can help if it's a slow leak.
 
When do you get water?
After sitting but no rain
After sitting after rain
After running the boat, no rain and no splash
How much water ( can you see the bilge pump cycle?
Are the scuppers below the water line at rest or when running?
Answers to these questions will help narrow down possible sources.
 
Which bilge front or rear? From bilge will unfortunately always have some water because it's the lowest point.
 
I had an issue with the deck drain bedding compound on a 228. The seals were broken and water entered the bilge when it rained and when water was on the deck during fishing. I would check the seals around the deck hardware first.
 
Could be a lot of things. I'd reseal the deck plates first (easy and quick). Check water type if you can (fresh or salt). Check pressurized water system if equipped. See if any cup holders are draining into the bilge area. The scupper hoses and clamps (should be double). You could install ball type thru hulls or temporarily tape with duct tape if in the water to see if one is leaking.
 
If you can determine when the water is entering the bilge, you will narrow down the causes. Yes, you can seal all the seams, deck plates, deck panels but if you think that rain water is leaking down, nothing beats a garden hose. Just flood the deck and check every now and then for bilge water. Start aft and work forward. The anchor locker lid and windlass are common places for water entry.
If water is accumulating only when running or while sitting at the slip, you have a whole different issue.