I normally refer to booking through an online agency as booking directly on their website online and not working specifically with an agent. But often when a person does get involved, they aren't licensed travel agents. (Not unusual for them to say they are when in reality they aren't.) However, one thing you really need to be cautious of is when they're selling a cruise for less than what they cruise line is selling it for; it's quite possible they could be discounting, which is something that is not allowed by the cruise line. If they're caught discounting, they could lose their credentials to sell for that cruise line and obviously not someone you want to do business with. Might save you some money but could end up costing you alot in the end. And if they say they're going to charge your credit card, run the other way! They should be serving as an agent for the cruise line and therefore they should be having the cruise line charge your credit card. Doing business any other way is just asking for trouble.
But when you call the number of the website or fill out the information and they pass you along to someone else, personally I have a problem with that. You should be able to call the number and get the agent you're dealing with in person. It should be their number and their email address listed on the website; not a corporate number or corporate email. I much prefer to do business with a small business person and not a corporation. That small business person is going to go out of their way to assist you as they want your repeat business and your referral; they deal in quality not quantity.