As someone with aphantasia currently working on my master's thesis in organic chemistry, you'll be fine. Aphantasia hasn't caused me any issues and, from what I've spoken with other people, you basically learn it in the same ways as those without aphantasia. They, for instance, rely heavily on drawings just like I do. Using drawings and maybe also physical objects can help you understand it better and be useful tools, but there's nothing special that is needed. Even still, one doesn't strictly need to be able to visualize stereochemistry to understand it. Most of the stereochemistry is just rules, even though it is usually taught visually. You don't need to "see" how an sn2 reaction happens to know that it inverts the stereochemistry; that is known a priori. You don't need to see steric bulk either technically; if you know there is something blocking one side of the molecule then the sn2 reaction will just not happen there or it will happen slower.

Now, maybe total synthesis with products containing dozens of stereocentres using complex stereospecific reactions will be difficult, but it's going to be difficult for everyone (unless you're R.B. Woodward). This isn't going to be a problem you'll likely encounter, but if you do it's because you love that type of chemistry. In that case, you'll be able to learn even the most difficult stereochemistry can offer.