1) Depends. I suspect that every system acknowledged to be part of the Imperium will have at least one 'habitable' planetoid, even if that merely means a research/mining outpost on a dead moon, but that there will be a number of star systems, even within a sector which hold nothing of value (when the cost of exploiting the system and hauling away the loot is taken into account), and as such are not acknowledged. I don't know about you, but I'd put 'worlds inhabitable by terrestrial life' pretty damn high on the list of valuable resources.
2) Ancient data from before the Age of Strife? The Imperial Tarot? Spectrographic analysis of the star from 'nearby' imperial worlds? Those are probably the best methods, shortly followed by hunches, then rumours. The astrographic map over a dartboard has a few problems- not least of which is the fact that even an incredibly fine dart, when thrown at a map of a useful scale, will leave a hole covering several dozen square light-years, quite aside from the fact that such a map is only going to be in two dimensions...
3) Apparently, if the third eye is open and uncovered, they can see the warp. Doesn't matter if they're in real space or the immaterium. Yes, that carries a risk of insanity, which is one reason they tend to wear the bandanna/blindfold bits. The exact manner in which they perceive the warp is apparently highly subjective, which raises questions I'll come to later. While in the warp (and, y'know, actually navigating) they take position in the Eyrie, remove the blindfold/bandanna, look around and either steer accordingly or pass instructions to steer accordingly. The Astronomican and similar psychic beacons may be used as useful 'fixed' points of reference, appearing as something bright and/or pure and good, depending upon the oeuvre appropriate to their own perception of the warp. The metaphor of a lighthouse is probably a good one, although probably imperfect and flawed- we are effectively blind men trying to describe yellow.
4) As I noted, given that every Navigator perceives the warp in a different manner, making charts and logs that are usable by more than a small fraction of Navigators (if not solely by their creator) would pose something of a problem. I suspect the various Houses have got around that by making trips with more than one navigator and agreeing on a shared terminology to describe the storms, flows and currents they 'see'. Since the early training jumps of a navigator are undertaken with a senior navigator as an instructor, the knowledge and terminology can be passed along (at the very least for the phenomena close to whichever system the training is nominally occurring). While I suspect that each House will have its' own codes, charts, logs and rutters (their own Navis Prima, effectively), there must also be a common code used by all Navigators, as there have been mentions of charts in the hands of the Imperial Navy (that could be read by the officers, not merely the Navigators), and there is no guarantee that a ship will have Navigators assigned to it from only one House for its' entire working life (to say nothing of the need to transmit courses between ships when proceeding in squadron),
The maps in the DH core book are, in my opinion, nothing more than fanciful pieces of artwork that have been produced from actual maps and charts in order to make certain Imperial officials and/or nobles seem far more cosmopolitan than they actually are, although it is possible that their differences can be explained by the maps' origin- different Houses, different mapping conventions.
5) Plasma drives, apparently, require regular refuelling- partly, I suspect, because they are not massively efficient and horribly fuel-intensive, and partly because they are always active, powering the ship in general. As to the nature of that fuel, my guess (and I regret, it must be only a guess, albeit one based on a wide reading of 'hard' sci-fi) is a slurry of deuterium, and/or possibly He-3 (the latter, I suspect, is more efficacious, the former easier to get). Logically, the ship must be able to carry sufficient to make at least one voyage, one way (which, given the nature of warp travel can probably be assumed to mean an absolute minimum of one month's tankage, with a six months to a year being preferable as minimums), plus sufficient life-support for the same (food, water and air, for the entire crew- a not inconsiderable amount of mass, altogether). I can see the urge to top up on reaction mass and life-support being a reflex action whenever a ship makes planetfall (or docks at a station or whatever).
Warp drives, on the other hand, require replenishment far more rarely, which is lucky, since the process of refuelling is said to be the most hazardous a ship can undergo, combat included. The fuel is, presumably, highly radioactive, as it is only handled by servitors wearing heavy lead suits (and are still burnt away by the energies coming from the fuel canister). However, since said fuel canisters are covered in thick layers of hoar frost, it seems likely that there is something even more esoteric than just plain radiation- some kind of psychic fuel as well, perhaps?
Sources: Eye of Terror, Execution Hour, Legacy, Star of Damocles and a short story whose name escapes me. Also- this