If you are upgrading from HALion Sonic (version 1.5), then yes. If you are buying it from scratch, then a boxed product is the only option because there are two DVDs worth of content in the first version that is not in the update download.
They might be “compatible” but it is irrelevant because programs saved in HALion will not be “visible” in HS or HSSE, regardless of their source. I tried to modify a program that is in the HSSE set in H5. I could not get it to become visible in HS2 or H5. I even tried to create a simple, one oscillator synth with no bells or whistles (just using the “init program”) and it was invisible to the lesser synths.
Programs you create in lower version synths will be visible in higher ones though. For example, a program created in HS will be available in H5.