I love e-junkie. You should definitely go with them, I use them for all my ebooks and ereports.
In answer to your questions:
1) If i add a product there how is the product protected so not just anyone can download and also if there are refunds etc?
The advantage of using e-junkie is that they store your file on their server and it's layered behind their security system. So instead of someone being able to nose around your website and find the file and grab it for free, they protect you from that. When you select how you want to sell your product it gives you the option of how much access you want to give to your product - how many downloads you will allow per customer, and/or what time frame you allow them to download your product (three days, five days, or whatever.) At the end of those parameters that you set the customer will no longer be able to download your product, giving you more protection so that people can't just forward your link around a thousand places and their friends don't get your product for free.
E-junkie is NOT a payment processor, however. They are a secure delivery and product storage service only. You have many options of payment processors that you can set up to mesh with e-junkie's system. The easiest is to just grab button code to create your own Paypal button. Customers click on your payment link, pay at PayPal, and then e-junkie delivers the product to them. You can also use Clickbank, Googlecheckout, and some others (I think 2checkout? Not sure.)
Because they aren't a payment processor you are still responsible for handling refund requests and dealing with the usual customer service complaints that will come up. So e-junkie doesn't allow you to bypass that. In pretty much all places where you want to sell your ebooks the customer service hassles and dealing with refunds will still come back to you - although with Clickbank the customer gets their refund directly from Clickbank. You still have to deal with the old "I didn't get my download link!" type of complaints though.
2a) Is the payment made to their account (the company's) and then i request payout via them or they pay me at a certain time of day or when i reach a limit etc or straight into my account? (if not any companys you know of that do that are as good?)
Again, e-junkie doesn't touch your payments - you still have to use a third party payment processor like Paypal, clickbank, google checkout, etc.
2b) It says i have to pay each of my affiliates.... what methods can i use to pay or do i choose which methods i want?
You would pay them out through Paypal - I don't think they allow other methods but I'm not 100% positive. So if you're a publisher it would be like the publishers do on Paydot.com - they set a time period where they promise to pay their affiliates, like 30 days after the end of the month, or the 1st of the month after the sale is made, etc.
3) Finnally what do they do to protect me from refunds and chargebacks etc or is that just impossible with anything digital except ebay and sitepoint with the not as described rule?
Again, since e-junkie doesn't handle payments they can not protect you from refunds or chargebacks. You'll still have to deal with your payment processor.
If you want to avoid ANY customer service duties you'll have to use a company like these:
Lulu.com (Allows you to sell physical print on demand books and also you can sell ebooks through them. But if you read the fine print of their contract they're a bit hazy about refunds and whether they even allow them or if they help you with them, so I'd snoop around a bit to be sure.) Also there is a waiting period before Lulu pays you. I believe they used to pay quarterly, I think now they might pay you monthly if you choose to accept payments via Paypal. And you can't have affiliates through lulu.com.
Share-it.com (Based in Germany, pays publishers through Paypal, has been around a long time. You can sell ebooks through them. Again I'm not 100% sure how much customer service they handle but I think they help with some things.) I don't think it's possible to have affiliates if your ebook is on Shareit but I might be wrong.
Booklocker.com (This is an American based print on demand publisher and they also allow you to sell ebooks if you don't want to sell your material as a physical book. They dont' accept everything submitted to them, though, so you'll need to submit your material and have it approved. They handle the customer service issues for you and also pay you your fees but there is a waiting period to receive payments on sales.) You can't have affiliates if you use them.
Lightning Source - This is a highly reputable company used by all the world's publishers. They are a print on demand publisher (they will print your physical books for you at a very reasonable cost.) And they also sell ebooks for you. With them you have the option of having them handle customer service for you. However, you will need to buy an ISBN number for each ebook you want to sell to get entered into their system. They also don't pay you right away because they have an official refund period - so I think they hold payments for something like 60 days and then pay you out the following month. One neat thing about them is that they make your ebook available in several formats, not just as pdf files. So if people, say, like to use a Mobi pocket reader or whatever they can get your ebook in their preferred format. Again, though, you can't make your ebook available for affiliates to sell via Lightning Source.
So if you want to sell products through your own affiliates, or you're seeking JV's in general, e-junkie is a much better way to go because people just sign up as your affiliate through e-junkie.
Hope this helps!
Dan