I have a 2000 named Ursa (she's a bear!)
the vacuum ports are there for balancing the carbs with vacuum gauges.
if the covers are cracked and leaking (or missing) you need to replace them. Should be able to find a package of something close at Advance Auto or similar parts store.
Before you run out and buy new intake boots and pull your carbs all off, use an un-lit propane torch while the bike is idling, and see if pointing the propane at the boots changes the idle speed. If there is a vacuum leak it will usually idle faster. Hold the torch with the bottle pointing up, so you get just the gas coming out, dont hold it tilted over or upside down so your get a stream of liquid propane coming out, that is too much. you can also run the test with WD40 or other volatile fluids, but it tends to make a mess.
On most Vstar bikes those rubber looking intake boots can look all cracked on the outside, and everyone sees that and freaks out. But it rare for the cracks to go all the way thru. Unless you test for vaccum leaks and are sure its the boots, dont jump on it because of the way it looks.
By far the most common problem with carbs bikes is a previous owner stopped riding one day and left the bike parked with 10% ethanol fuel in the tank, and after just a few months it breaks down and starts clogging things up. If the bike will run at all you can try putting a carb cleaner in the fuel, run the bike a hundred miles or more, and if the fuel is running thru the ports and jets at all, it might clean them out, and that is all you need. A bottle of Seafoam is $8 at walmart, and its enough for 16 gallons of gas.
The other thing: dont pay much attention to how the bike idles when you first start it - it takes several miles to warm up.
BTW, these V4s with the 4 independant exhausts sound like they are puttering when they are idling, that is normal. If its running well when you get on it, it might just be you need to get use to the sound of the engine... and maybe adjust the idle speed a bit.
Good deal on your new royal star - there are a lot of them out there, and they tend to be insanely reliable. I got mine last fall, and hardly ever see anyone here posting problems or issues, most people that have one just ride and ride and ride.
EDIT to add: here is recent thread talking about the boots, with a photo of one sliced down the middle: