Hi Manogr,
Well, late Aug/early Sept is approaching the peak of tropical storm/hurricane season in the region. Although the risk is relatively small, it is something you'll want to consider.
It will be quite hot & humid at this time, with both indexes likely in the upper 80s, lower 90s. But, so will the rest of the greater Caribbean. Rainy season doesn't start in earnest until into October. While you may have some rain, it most likely will be in the form of passing showers, often in the afternoon or evening. In any event, diving on Roatan is very rarely curtailed just due to rain.
As for the pretty much ever-present no see ums & other insects, you simply need to be prepared to deal with them. The below is from in my "Ask RSD" column in the Oct '99 issue of "Rodale's Scuba Diving" magazine:
"Sand fleas or 'no see ums' can be a bother. There is great individual variability in both allergic reaction to bites and in how attractive one is to insects. If you are high on both indexes, your dive vacation can be a nightmare.
The bother of insects can be substantially reduced by these precautions: (1) Wear long sleeves and pants, avoiding dark or bright colors, especially at dawn and dusk. Protective clothing such as the "Buzz Off" brand can be useful. As an extra precaution, you may treat clothing with permethrin; (2) Try to stay indoors at dawn and dusk when many flying insects are most active. When making reservations, make sure the resort has screened windows; (3) Wear insect repellent. Many report that Skintastic and Skin So Soft are effective against sand fleas, although the best protection against these and other insects is full strength DEET. Look for it at military surplus outlets and hunting and fishing supply stores; (4) Avoid scented toiletries and perfumes; (5) Upon arrival, treat your room with a bug bomb such as Shelltox or Fish. You can touch up with spray after that as needed.
Precautions such as these can go a long way toward insuring your comfort, although they of course don't guarantee that you will not get bitten. It is therefore wise to take along whatever medications which you have found safe & helpful in treating bites, e.g., Calamine lotion/cream, hydrocortisone lotion/cream, nonsedating oral antihistamine.
Remember that if you don't get substantial resolution from self treatment, have a severe allergic reaction, or the eruptions seem to get progresively worse or infected, you should seek medical attention in a timely manner."
Hope you found this helpful.
DocVikingo