why was there only one engineer abourd the juggernaut on lv 426?

A lot comes from some inconsistency in how they even Plan the Movies and every element within them...

Alien gave us just the One Pilot.... RS had after Aliens said he would have like to had explored the Derelict and why it was there and mentioned about finding out what happened to the other Crew of that Ship.

This thus tells us RS had a Vision, maybe not when he was working on Alien but certainly a long time before he began work on Prometheus that the Derelict had more than ONE CREW

Alien: Engineers was the first attempt at a RS Prequel and this Draft, introduced the Engineers and Juggernaught and this Draft indeed explained there was 6 Crew  and a Sperate Area where there are Sarcophagus that suit the Engineers with Flight suits , they do not line the Walls... the Hybernation Chamber has 4 Cryo-Pods...

Paradise draft by Lindeloff again informs us there are 6 Ghost Engineers in the Juggernaught Play Back and again there are just 4 Cryo-Pods however.

So indeed it is a little bit strange....

Do the Engineers Rotate a Shift Pattern between who is awake and who is in Cryo-sleep are there other parts of the Ship where Engineers have other Cryo-sleep pods?

All i can conclude is that the Juggernauts have 6 Engineer Crew, hence the 6 Space Jockey suits...

As for the Derelict and its differences, again on Film we see no Cryo-Pods, but we cant confirm there was just the One Crew Member... so again maybe the Derelict has a different Cryo-sleep set up but its anyone's Guess to where this is and how many Engineers this ship held.

EDIT:

I forgot to add that Prometheus as far as i recall there are 4 Engineer suits in the Hallway, but there a few Hallways leading to the Central Control/Pilot Chamber and the Ghost Engineer Scene had 4 Engineers but they appeared in pairs from either side of the room.

Alien Covenant as far as i remember had 6 Engineer Space Jockey Suits.

In Prometheus the last 4 Engineers which survived the outbreak entered their hypersleep-pods after sealing the room.

Only one hypersleep chamber was functional (and not contaminated) after 2.000 (+-) years , so only one Engineer survived at LV-223.

The same could happen for the space jockeys "friends" on the derelict ship which crashed on LV-426.

He was the only pilot, got chest-bursted,crashed, all other alive Engineers/SJ's got killed in their Hypersleep-pods in the crash.

The juggernaut on planet 4 is a special case here.

There where probably no Engineers aboard here since Dr.Shaw and David used it to travel to planet 4 / Paradise.

They would notice it after years/months of living there in limited space.

I think the answer lies in the practicality. I believe Ridley starts set building based on his story boards, WAY before scripts are written, and certainly WAY before they are finished and the screenplay is completed. Because of this, and the film's budget, the sets actually determine the story, and the required rewrites are based around the sets, rather than the other way round, at least on Ridley's films...or so it seems.

This is very true Starlogger

Production had began on a Alien Prequel before it was re-wrote by Lindeloff to become Prometheus and then become shot... so the Production on the Chest Busted Props and Juggernaught could have been well under-way before the movie Draft was finished and shooting began... this could explain why no explanation is touched upon with the Chest Busted Cryo-Pods in Prometheus etc

In A:RoP they found more than one dead "Engineer" on board of the derelict.

Indeed Tiwaz that book maybe took some of the information and ideas RS had for how he would have done a Prequel.. many many years ago.

Regarding if this is Canon i think the Books can be but then can be taken from Canon too... but themes and ideas in the Books could be explored in future and so we cant rule out RS showing us the Derelict had more than ONE-CREW

RS comments about the Engineers coming back into it, does not mean the chances of this are Good, as opposed to it being ONE Human or Synthetic Pilot.

Some people might not like it but it IS canon and sold as such, until it is retconned by the next movie, novel, comic etc.

Starlogger - 

What an amazing observation regarding the sets.

Take A:C for instance - Now one of the big let downs was the lack of dialogue commenting on those amazing surroundings.

Some of the greatest sets built yet the actors just walk by them as if they werent there.

So your theory fits because if RS does work that way that may explain the lack of dialogue because the sets were built while the script was written and so may not of emphasised the importance of a particular set because the story had its own, SIMILAR path

@sherris, To play Devil's advocate, they had far more important things to worry about than architecture! Personally, I'd have loved a 4-hour movie, but that's really not going to happen these days.