I use to spend every day of the season on Joppa Flats guiding for stripers (out of a canoe, sometimes a kayak and then a Dory)... The first thing to watch out for when in a small craft out on Joppa, is the other boats.
You don't have much for rocks that you need to worry about (if you don't have a prop), but wind and current are the things to stay aware of.
The next is the boat ramp at the sea wall is great, but at 3-4 hour after high you will be dragging in your kayak to get back in and TAKE MY WORD ON IT, you don't want to be in that thigh high mud...
If you are new to fishing the area, stay out and away from the channel and stay on Joppa Flatts and you should have no problem... You can always hire a guide (some one like me) to show you the ropes and save you years of figuring it out yourself...
One more tip, the area is best fished morning, evening and night. You can catch fish during the day, but most of the time the numbers are very low...