Strategic Operations has a whole section on detecting objects in space.
Jump signatures are detectable from quite a distance, so it's hard to disguise the fact that something just popped into the system if the local defenders have enough tech to look for that sort of thing. That being said, the detection range isn't infinite, and if you jump in far enough from the system and are willing to spend a while getting to the target with maneuvering drives, you could make a stealth insertion.
You'd want to keep your engines pointed away from the enemy at all times, though, since the light and other emissions from the drive flare are also detectable from a fair distance. This makes the whole 'accelerate to the midpoint, flip over, and then decelerate the rest of the way' technique somewhat non-stealthy.
And then, of course, you'd want to maintain radio silence and shut down your active sensors.
If you do that, you're a cold, silent needle in a very big haystack. During the...War of 3039?...a FedSuns Fortress-class DropShip got lost during an assault. Dozens of ships combed the system for weeks looking for it, with no luck. And that ship would've been trying to be found. Another example - the Blakist base at Gabriel, in the Odessa system, maintained operational secrecy for centuries, moving ships in and out of the asteroid shipyard in the remote reaches of the system without anyone detecting their presence.