The weather and time arent "Hackable" really.. weather is absolutely not because its controlled by the server. you can fool your client into thinking its storming but nothing would actually get struck by lightning or so time is same, server still has its own tracking, but you can trick local client into showing day time but monsters will still be spawning... so the only thing you can really "hack" is giving fake light during the night time, but servers not going to know anything about what your doing.
Once on smp3 I was taking a group of poeple to the end and there was a HUGE storm! There was 5 bolts at once! It lasted two mc days We made a dirt shak to hide in. It was so fun. We where all to scared to go outside lol
oh and to answer the root complaint: Blame Mojang... They added super storms in 1.3 which is what you are seeing. I tweaked our configs to lower the chance of these happening though so they happen less than vanilla.
