an entry level bike is not likely to have a full shimano groupset. often brakes will be tektro or unbranded, and the hubs will almost certainly be generic and married to an alex rim or the like.
provided the drive train is mostly shimano with sora levers and mechs, you should be ok. if the brake calipers are rubbish, a set of tiagra calipers won't cost a fortune and will make a big improvement.
having been through the process of having bought a bike and then upgraded it over time, i would say that you'll save money by buying a better bike to start with. however, if you prefer to spread things out over time, or you don't want to commit too much in case you don't get on with cycling, it's a reasonable way to go, especially if you can buy a complete groupset in the sales.