If capsules aren't removed during explant due to capsular contracture, will this affect the way my breasts look?

Sometimes not all of the capsule is removed
following explants. The reason some of
the capsule is maintained is that it does add to the breast volume and often
with explants we are trying to maintain volume as much as possible.If there is any area of
thickened capsule this is normally removed and I think it would certainly be
worthwhile talking to your surgeon in detail about the pros and cons of capsule
removal in your case. I do wish you the
best of luck with your surgery if you decide to proceed with it. 

Generally speaking, unless the breast implant capsules have thickened and/or are otherwise symptomatic, there is no indication to have them removed. Your question indicates that you may have capsular contraction;  generally, best to have this thickened capsule tissue removed during the surgery. On the contrary ( unless indicated), capsulectomy can expose you to additional risks, such as bleeding and some breast size loss.
Having said that, I often remove a small segment of capsule tissue when removing breast implants ( even when not encapsulated) with the hope that this maneuver will help with fluid resorption (and help prevent seroma formation). I usually use drains also.
What your breasts will look like after explantation depends on several factors such as: the quality of skin elasticity (the better the elasticity the better the skin will bounce back), the size of the implants used (the larger the implant the more trouble you may have with redundant skin), and the amount of breast tissue present at this time (which may have changed since the time of your breast augmentation).
Life experience since your breast augmentation procedure, such as pregnancy or weight gain weight loss, will potentially influence the factors discussed above. If you take these factors into consideration and apply them to your specific circumstances you may get a good idea of what to expect after the implants are removed.
Patience is definitely indicated after removal of breast implants; it will take many months for the skin to “bounce back” and for you to see the final appearance of the breasts.  In the meantime, I would suggest that you continue to follow-up with your plastic surgeon on a frequent basis;  he/she will be in the best position to rule out and treat complications such as fluid accumulation,  and will be in the best position to provide you with meaningful reassurance.
I hope this, and the attached link, helps.

Hello! Thank you for your question! It is a matter of surgeon preference as well as what is seen during your procedure that will determine whether or not a complete capsulectomy is performed. If significant capsule formation is seen intraoperatively, a full capule removal may be warranted with a drain in order to completely remove all of the tissue and allow better adherence of your breast back to its normal anatomic position down on your chest wall. If minimal contracture is seen, it may be possible to leave the capsule, or place cuts within the capsule to allow better adherence.

It truly is dependent on what is seen with your capsule and the issues that may be causing you to have such a procedure (e.g., contracture from rutptured implant vs pain vs simple pocket adjustment, etc). Without knowing your issues and without an examination, it is difficult to tell you what may be the best thing for you. I tend to favor performing capsulectomies in order to create a fresh pocket, reshape the pocket, allow better shape and adherence of the overlying breast. I would discuss your issues with your plastic surgeon who will assist you in determining the right modality for you. Hope that this helps! Best wishes!