Probably not 8" diameter ports- the deck probably isn't much more than 8" wide in that area. Common access port sizes are 4", 5" and 6". But regardless, port holes in front of the front pylon (or in front of the front crossbar) are generally considered to be a no-no. That's not to say it hasn't been done, but there is a lot of load in that area, so ideally, you would be better off putting the port behind the pylon.
If the price was right, it might not be a deal breaker, but it would definitely be a concern.
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What are the main differences? Is it worth the money for a newer boat?
The main difference between a newer boat and a 25 year old boat is going to be the overall condition of the boat. Think 25 year old car vs. new car. Now it's possible that the older boat has been sitting unused for a while and was well taken care of and that the 2005 boat was beaten on. But statistically speaking, the odds are that the new boat is simply in much better condition.
Otherwise, the general design of the Hobie 16 has been unchanged. Some of the systems have been refined to work a little better, but overall, there won't be any significant design differences between the boats (especially for someone with zero sailing experience).
By the way, I would still recommend that you seriously consider getting a dinghy to start out with (or possibly a Hobie Wave / Bravo if you're set on getting a cat). You'll have a lot to learn and those types of boats are specifically geared towards beginners. They're much more forgiving.
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