Prostaglandin analogs may cause changes in iris color and eyelid skin, growth of eyelashes , stinging, blurred vision , eye redness, itching, and burning. Beta blockers' side effects include low blood pressure , reduced pulse rate , fatigue , shortness of breath, and in rare occasions, reduced libido and depression . Alpha agonists can cause burning or stinging, fatigue, headache , drowsiness , dry mouth and nose , and also they have a higher likelihood of allergic reaction. Carbonic anhydrase inhibitors may cause stinging, burning, and eye discomfort. 
You are exactly right in your thinking. Different drops are used to dilate eyes. Tropicamide (mydriacyl) is the most common drop and it comes in two strengths, % and %. The % will not last quite as long but it is not a large difference. Tropicamide will dilate the eyes and interfere with near focusing. Phenylephrine is often added as a second drop with mydriacyl to enhance the dilation. Phenylephrine enlarges and hastens the dilation but has no effect on focusing and usually does not prolong the dilation. Paremyd is another drop containing % hydroxyamphetamine and % tropicamide. It does not dilate the eyes as well but tends to last a shorter time period and not interfere with near focusing as much. Longer lasting drops include cyclopentolate and homatropine. They have a longer mode of action and exert significantly more interference with close vision. They are usually used for children.
Management of acute endophthalmitis requires a rapid diagnosis and appropriate treatment or referral. Most cases of endophthalmitis are managed by vitreoretinal specialists who will take a sample of fluid from the eye for culture and inject antibiotics or antifungal agents into the eye on an emergent basis. In cases of light perception vision only, vitrectomy is recommended in addition to culture and antibiotic injection. Cases of endophthalmitis can lead to a complete loss of vision and even the eye if not treated rapidly. However, it is possible to retain good vision if treatment is timely and successful.