The two reasons mentioned above - giving the impression of a great bargain while still protecting your actual minimum selling price and to lower the amount paid in eBay fees (they get a percentage of the sales price) are the primary reasons sellers do this.
I don't care for it because I think it makes the seller look sleazy (I tried padding the shipping once and got nasty questions from someone, decided it wasn't worth risking the feedback as a little seller. A bigger seller isn't as hurt by a little bad feedback).
One possible advantage to a buyer would be if it was one of the rare instances when sales tax would apply, in which case the shipping and handling is not taxed.
One warning on the "Calculate Shipping" box, when a seller lists that option, they can include any handling charge they want, so don't assume that isn't padded (I have seen instances when it was very padded).
I won't buy from a seller who doesn't list shipping costs up front unless I can email them ahead of time, and I get an appropriate response.
Like others said - Read the description very carefully. I have caught other instances of potential fraud that way - like the ass that kept advertising "Information on how to get a Playstation 2 for free." His ad was written very, very cleverly so it really looked like a real machine was being offered (with a 99 cent starting bid), but all he sold was a link to one of those websites where you have to complete an offer to get a free gift (spend money). It said it was info, but I watched him for a while (and kept reporting it to ebay) and he got as much as $140 for that "info." Almost all the bidders were newbies, and all of the winners had either never bought anything, or only bought on ebay once or twice before.
Oh, and warning on those "complete an offer for a freebee" sites. I actually did one of those (wanted that particular offer anyway) but never got the gift.