Depending on your head unit and speakers, the new head unit may be better suited to powering your new speakers, rather than the original amp.
Instead of running all new wires from the head unit to the new speakers, it sounds like they have just bypassed the amp by taking the output from the head unit, and jumping it straight across into the speaker wires. (easiest to do right at the old amp)
I wouldn't be overly concerned about it, if they are a professional shop, they know what they're doing, and I'm sure they'd be happy to answer any questions you might have if you approach them directly