I used to keep a 42' boat in Anacortes. It's a very nice marina, easy access from I5, and in the middle of the islands. Having said that, the San Juans are a tricky sailing territory for a variety of reasons:
1. Currents are high during spring tides, in some places up to 10 kts (deception pass). So you need to plan your trips and routes ahead of time. We have double tides in the NW, meaning two cycles per day, so the time windows are half of what they are elsewhere.
2. The main channels have large vessel traffic coming through. Tankers moving at 20kts. Only sail in good weather with visible conditions. Their radars will not pick up a hobie kayak, unless you have an aluminum sail
3. Rip currents and whirlpools. I have seen some pretty strong rip tides and whirlpools in the San Juans. They got my attention on a 42 foot boat. I would be nervous in a hobie kayak. They occur in known places, so you can avoid them, but you need to do your homework.
4. Weather changes are rapid. I sailed the straights in 42kts of wind, with snow and ice. The swell can get huge, 20+ feet, so again, do a little bit of forcasting.
By now, I sound like a chicken, I know. Don't let this discourage your plans. The islands are great to sail in and great to kayak in. There is tons of wild life, better seen from a kayak than on any other boat type. I have taken paddle kayak trips around san juan island and it was just fabulous, bald eagles, seals and cubs, orca whales - very humbling.
One thing you don't have to worry as much about is low tide.
In a big boat, certain places become inaccessible because of keel/draft.
Final ideas: When you go, take a water proof marine radio (channel 16 is always at your service) and file a "flight plan". Tell someone what your plans are, so that this someone can call for help, if things go bad. This may sound more dramatic than it is. It's just a good "habit" and no-one will ridicule you for doing it.
The San Juans are a superb sailing ground, and I am sure you will love it.