Bookshelf speakers tend to be a better value than tower speakers mainly because they’re smaller, which means less production and shipping cost. There’s also just more of them produced, which means more competition, which ultimately means better deals.
With a subwoofer in a system, it allows for the main speakers to focus exclusively on the mids and the highs, and this naturally lends itself to really optimizing around a 2 way, single crossover design with a tweeter and a woofer. This can be done well and inexpensively within a smaller bookshelf speaker.
Tower speakers can accommodate larger woofers, or more of them, but unless they use a 3 way design with two crossovers that allows for a dedicated subwoofer that’s built in, they’ll generally under perform with the bass. 3 way tower speakers can certainly be excellent, but they tend to be rather expensive, main problem being they have to be big enough to house a decent sized subwoofer. With an external subwoofer, however, it can be nice and big on its own, and the bookshelf speakers don’t have to worry about containing it obviously.
You might think an external subwoofer would call for a more powerful and expensive receiver, but most home theater subwoofers are active or self powered – all they need is a standard RCA connection, which just about any receiver will have.
The disadvantage of bookshelf speakers is that they’ll need to be placed or mounted above ground level somehow, whereas tower speakers just have to be put on the floor. Tower speakers look pretty cool too, and some people do care about the aesthetics and decor of their sound systems. Keep in mind that you could always pair a subwoofer with tower speakers too, it’s not like there’s some rule against that.
And of course, the ever pertinent consideration is that prices just fluctuate so much in the audio world. If you see a good pair of 3 way tower speakers for cheap, or pair of 2 ways with good specs on par or better than the bookshelf speakers you have an eye on, then by all means that might be your best choice at the time.