I'm planning at trip to Botswana, Namibia and Zambia in januari to april. Have checked the weather in the Lp and the words "Wet season", "stormy period" and "hot" comes up alarmingly often. So how bad is it? Are there monsun rains that flushes away roads or just occasional rains? And how hot is it? Is it still worth going there or should I do the trip at a different time?

I can speak for Botswana only, as I have been there in January and March several times - and love it! whether yu go this time of year or wait until the dry winter season there depends on what you want out of your trip.
Botswana is absolutely a year round travel destination, but during the green season (Nov-March) you do need to know where to go to maximize game viewing if that is your intent. The semi-arid Botswana landscape greens up this time of year; calving season and birding are at their height during this season - making it a photographer's dream. The Savute and the Central Kalahari Game Reserve offer the best wildlife viewing this time of year. The combination of epic scenery and wildlife/birdlife in Chobe and parts of the Okavango Delta (north) and the Tuli/Mashatu area (far eastern) are stunning.
Self drive in Northern Botswana during this time is not recommended, as the rains can make the "roads" in the more remote regions difficult to navigate or impassable. It is hot this time of year - but no different than USA summers in the Mid-Atlantic area (ave. 60-70's at night/low 90s during day). Rain is normally confined to an afternoon thunderstorm (and there is nothing quite like the majesty of an Africa thunderstorm), though occasionally rain can last all day. The heaviest rains usually fall during Jan-Feb.
This is the time Botswana offers "green season" travel packages - making a trip during this season a great value. You can find many green season travel packages at: http://www.botswanatourism.us/travel_specials/green_season.html.
hope this helps1
