Two thoughts.
Do you think it likely that you will have crossover customers? Someone who comes to your shop for graphic design items...but then decides they want web design products? I've tried it, myself, and selling two rather different products did not really work. I've never had, for example, a customer buy BOTH an ornament and a digital coloring page. Having two different products in one shop is not a problem....I just haven't seen an advantage.
Will you have sufficient listings to fill two shops? How many graphic design listings can you foresee? If you will have well over 100 graphic design listings (that fall into different categories), then you may wish to have a separate shop for the web design (so you can retain the categories to differentiate between graphic designs). As has happened with my ornament shop, at peak season, I have over 400 listings...and I want the ability to use every category available to me (why can't etsy provide more?!). I haven't liked devoting one of those precious categories to my "other artwork" because an additional ornament category would probably be more useful.
Now, if you only foresee, say, a reasonable number of listings per graphics and web design, maybe keeping all in one shop is the way to go. One shop is much easier to manage than two. (I have two)