Im planning on starting the module this week. My players are 4-5 rank, and there are scaling in the module for some of the encounters.

But it seems to stop halfway through the adventure. Nothing on some of the most important encounters, like the Hektates, in the Pax Macharia and the Dei Phage. Has anyone played and scaled this encounters, or does anyone have ideas and suggestions?

Spoilers ahead

I ran the adventure with a big group. The core members (3 of them) were rank 4-5, and the rest were just above starting rank. That said, we only really had two combatant characters, and in many fights the non-combatant characters did stuff like hide, fall to their knees and prayed to the Emperor, etc.

It all depends on what type of group you're playing with, their equipment, skills, willingness to engage in combat and such things. I did notice the same thing you did, the level scaling all but stops after the first chapter. Some fights took a long time to finish, Gustavus Hekate being the prime example, while they found others, like Nikea Hekate, to be a cakewalk. When the characters reach the Haematite Cathedral, it seems like all "trash mobs" are extremely easy to dispatch. Nikea Hekate's henchies are broken down servitors that fight with rusted serving trays (?), and will be trivial for anyone above starting rank, imho. Same goes for the mutants in the Asylum wing. If you're running with a rank 5 group, you'll need to bump them, and employ unusual tactics, since most enemies will only use melee attacks.

The last part, when they're off to face the daemon, will largely hinge on what type of group you have. My group had a Sororitas, which had the ability to counter the daemonic auras that the furies and the Dei-Phage employ. It'll also be somewhat dependent on the players making the right choices in fighting the daemons, otherwise the fights have potential to be really challenging.

I've recently started a group through Black Sepulchre. The PCs are Rank 4, pushing 5, and there are four of them; two Tech-Priests, a Scum, and a Psyker. The players are quite intelligent, have been gaming for many years, so there's nearly nothing they haven't seen in terms of combat encounters. Dark Heresy has a different combat pace, though, and I find they tend to take the straight forward approach 99% of the time, meaning I very rarely see PCs Feinting, Maneuvering, Disarming, etc. I think the main reason for this is because, as long-term gamers, they want to see how the initial Rounds of the combat play out before committing to action, so they run their PCs on "auto-pilot". Once things get rolling and the initiative steps are set, they have a pretty good idea how things will play out (barring cruddy dice), and all that fancy stuff beyond "beat it with a stick and burn it with fire" is flashy and delays the death of gribblies.

The PCs aren't huge anvils of doom, but the players love to hammer their way through, so I need to keep things lively. The mutants in the Sanitorium (Gustavus' experiments) are one example. I wanted them to be a threat, but not so much that the PCs bog down and become timid mice due to being heavily wounded, so I played the mutants as "spectres", half-living creatures representing the angry and confused spirits if Gustavus' patients. They crawled the walls and ceilings, a la Gollum-style, chased after PCs by running up the bottom of the stairs, and I changed their attacks so that 1( they would not be Primitive, and 2) each attack had a Phase-like Trait, scoring a Pen value of half the armour in the location hit (rounded up). Not as good as a Warp Weapon, while still giving the PCs a sense that their armour was working. They took pennies and nickles in damage, but the creatures do have Fear 1, Swift Attack and can easily maneuver to outnumber them, so it looked "even" on paper. Turns out, even with some cruddy dice (on both sides), it was even, and the PCs came away from the encounter with a few scratches and bruises, a healthy respect for any future denizens they come across, but ready to continue searching the Cathedral.

Scaling takes a practiced GM's eye. You'll whiff stuff along the way, and you'll over compensate too, but it'll come to you.