How long can i cook a bone in Pork Shoulder

The recommended cooking time is only a guideline. There are a variety of factors that influence cooking times in a substantive manner. For what it's worth, water in the water pan is not one of them.

The purpose of the water in the water pan is to act as a heat sink, in order to prevent temperature spikes. Anyone who claims that it helps keep what you are cooking moist should be summarily ignored. One of the more likely scenarios is that the thermometer is either inaccurate, or it is not an accurate reflection of the area in the smoker where the meat is being cooked. There are no guarantees that the temperature you read at one point is constant throughout the smoker. In fact, it is almost a certainty that the heat sink (water) will cause a cooler area in its immediate vicinity. This is pretty common in the Weber Smokey Mountain, and is why I don't use water in mine.

I would suggest some things:

1. Check the calibration of your thermometer (get a temperature reading with the probe in boiling water).
2. Put a thermometer (an oven thermometer will do) in your cooking area, to get a sense of any discrepancies between the lid and the cooking area.
3. Crank up the heat, if necessary (250f is still "low and slow").
4. Experiment with not using water, to see if that makes the heat distribution more amenable to cooking in your smoker.

Now that you have some cooks under your belt, the time is about right to tweak your methods to your liking.

According to Modernist Cooking Made Easy (emphasis added):

For medium rare cooked pork shoulder, the meat should be held at 135°F or 57.2°C, while medium cooked meat is done at 145°F or 62.8°C. If a traditional well done shoulder is desired, it should be cooked at 155°F or 68.3°C. No matter what temperature range is used, the pork shoulder should be cooked for 1 to 2 days. For a crisp or well done outer part, sous vide pork shoulder may be finished by searing, grilling or torching.

Note that to safely maintain and control temperatures this low for the sustained period of time, you must have a proper sous-vide setup, with a means of maintaining the temperature of the water bath.

Even at 135 F, over several hours, the method is safe because the killing of pathogens is a function of both time and temperature.

Similarly, the conversion of gelatin to collagen which gives slow cooked pork its unctuous texture is also a function of both time and temperature. While in more traditional cooking methods (oven or barbecue), reaching internal temperatures of about 180 F is necessary to get collagen conversion in a reasonable period of time, it can be done in the truly extended time periods sous-vide cooking makes possible.

For more traditional cooking methods, about 225 F is about as low as you want to go

See also:

• Why would a pressure cooker shorten a braise time? which looks at this question from the other end, making the conversion more rapid, and describes collagen to gelatin conversion in more detail.