It's unclear if nuclear energy would be a choice propulsion for a space faring civilization. It's possible, but it's not the only option. That said, if it was the method of choice, it's not at all clear to me that it would be easily detected.
Let me preface this with stating that I'm not an expert. There's two kinds of basic nuclear engine that could be used for space travel, closed or open. An open nuclear propulsion is much simpler. Basically explosions are made outside the ship that propel the ship by force from the explosion. Tiny nuclear pelots are detonated and that's what pushes the ship.
The other method would be an internal nuclear engine, well insulated that generates electricity and electricity generates magnetic fields and presumably ion thrusters that push the ship. We wouldn't detect nuclear energy if it's internal and insulated.
The Orion ship that you mention in your question wouldn't make one megaton explosions, but many smaller explosions. It would carry more fuel than 1 megaton, but it would use it for tiny explosions over it's journey. Space is also full of Gamma radiation, so I don't think gamma radiation would stand out.
You can't look for gamma-rays from Earth's surface because the Atmosphere blocks most of them, so you need a space telescope and our best space telescope for that is the Fermi Gamma-ray Telescope. https://fermi.gsfc.nasa.gov/ (having trouble with linking, not sure why).
The Fermi scans the entire sky, so it's really more of a survey than a telescope, and gamma ray sources are still being studied, with 31% (per chart) listed as unknown sources. https://www.nasa.gov/mission_pages/GLAST/news/gamma-ray-census.html
I don't think our current equipment is close to detecting a 1 megaton nuclear bomb a few star systems away, much less an orion type spaceship. I think it's too few gamma rays at several light years distance. Perhaps with better equipment we'd have a shot, but I don't think we're anywhere close to that now. That's largely a guess though, I'm not an expert on the subject.
Edit
There's something wrong with my account, I can't comment either, so I'll post it here.
Your assumption is that 1 megaton is large enough to be visible from lightyears away - by gamma ray telescope. I'm not sure that's true.
1 Megaton = 4.18 x 10^15 Joules.
1 Joule = 6.24 x 10^18 electronvolts.
So, 1 Megaton in explosive energy (and not all of it would go to gamma rays, but a decent fraction). But ignoring that fraction, 1 Megaton = 2.61 x 10^34 Electron volts.
The surface area of a sphere 4.1 light years in radius (the distance to the closest star), 4 Pi r^2, where the radius is 3.88 x 10^16 meters, is 1.89 x 10^34 square meters.
So a single megaton blast 4.1 light years away would average out to a bit over 1 electron volt on a 1 meter gamma-ray telescope. A typical gamma ray is thousands of electron volts, so unless you have a very large telescope, there's a good chance you wouldn't pick up a single gamma ray from a one megaton blast 4.1 light year away, or maybe you'd pick up one if you were lucky.
4.1 light years is very far. Far enough that a telescope, unless it was enormous, would have a hard time seeing a nuclear blast that far away, and that's the closest star system.
Corrections are welcome but that's what the math looks like to me.
