Checking is one thing, but replacing themes and wallpapers (which involves hacking to do so) to promote your own company is completely different. Wouldn't you agree? In this case, more likely than not, had it been left alone, the GBA emu probably would have run fine.
Maybe it's just me, but when I buy something new I want to receive it that way. New & untouched. If I buy a TV, I don't want a salesperson to open it first and play around with its settings & configuration. If I buy an iPod, I don't want a salesperson to load it with songs that they think I should listen to. Likewise with a mobile phone, I'll decide what settings to apply and what themes I want to use. I want to break the seal on the packaging. Its peace of mind for me.
I'm not attacking DDU, I just think its odd to tamper with new goods before selling them.