The zen_draw_separator function isn't used by Zen Cart on the catalog side of the site (the only side that search engines should be spidering).
It's a throwback to table-based layouts when transparent pixels where used to keep things in place. Template Monster went through a phase of using them in place of padding and margins, even on tableless layouts. Goodness knows why - I suspect they had people who hadn't quite grasped proper layout. But I thought they'd got past that now.
Point is, that this function shouldn't be being used anywhere that it matters. So your options are:
- re-code the template to remove the function call or
- re-write the function not to call the zen_image function that inserts the alt
However, that alt is probably doing you more good than harm. It's impact on the code to content ratio will be miniscule. It's absence would mean that your page would not validate. I'm guessing that if there's any effect at all, the latter would have the bigger benefit, but that neither would really be noticed.