Well , its true that the wordpress theme making community is getting bigger and bigger and anything that is growing such rapidly its going to have its flaws. The main reason behind these encrypted code is because of theme sponsoring. Sponsoring?? , well as a wp theme designer my self , ive had a few sponsors my self, for my wordpress themes.
Many designers make wordpress themes just to get sponsors , ive seen many people making only one theme , changing the colors and the header making it a new theme ( so they say ) and get sponsors , the average sponsor link is worth $30-40 and a sponsored theme has 3-4 such links making a revenue of average 150$ / theme .
So i havnt explained the reason , well the 2 main conditions that are required for a theme to be sponsored by a sponsor are
1: Encrypted footers
2: Heavy promotion
As you may or i must say definitely have read this informative article , most of new wordpress themes contain such encrypted code. Whats behind them is links, yes in most cases and i am not justifying the acts of people who have done things in the above articles, but am saying that in this encrypted code are hidden sponsored links which the sponsors have paid for. So why do people encrypt the footers? well if you see some one honest using a free theme they dont remove the footer link as they know its someones hard work , but most of the people remove the links in the footer taking the credit them selves. So in a nut shell its basically done for sponsoring.
And as said in the article , you should download themes from sites of the theme makers or atleast download from a reputable themes gallery.
Have a nice day .