In 1948 what was clearly different is that the majority of Parliament, or at least the Commons, was onboard. As I understand it the 1948 prorogation was to artificially create the number of sessions needed to push through the Parliament Act against the wishes of the Lords. Meanwhile the 1997 prorogation led into a General Election, so although there are clear suspicions that the motives were a bit untoward it was also unarguable that Parliament had to close a week later anyway for the GE.
What is different this time depends a little on whether you take the Government seriously or not as to their reasons. Every Brexit supporter on AB was cheering the prorogation as a means of getting shot of those pesky MPs for a good month, which is, not coincidentally, exactly the reason that Johnson *doesn't* want the prorogation to be attributed to. So if it turned out that it was the former, rather than the QS, then what's different is that Johnson lied to the Queen when he gave his advice.
What is also different is, yes, undoubtedly the tense political atmosphere right now: I don't doubt that a few Remain supporters will use every trick in the book, and some that aren't to try, and defeat the Government on the No Deal point at least. Pushing through legislation in a day or two is highly unusual, and probably generally unwise. But it's not like Leave supporters aren't trying similar things: Theresa May's government was throwing all sorts of procedural devices to try and keep Parliament's noses out of their business.
Oh, yes, and what's different here is that Johnson has no majority. So it's a minority government that has no real authority any more nevertheless telling Parliament that they can get knotted.