Would a hypercardoid mic also be preferable in outdoor shooting?
You use a shotgun mic outdoors because of its superior off-axis rejection; in other words it has a narrower pick-up polar pattern than other mics. This is preferable when shooting outdoors because, if handled properly, picks up less (rejects) sounds to the sides and more of what it is aimed at.
Also would I be able to get decent audio quality out of a mic that is run directly into the DSLR rather than having a separate audio recording, I realize that the quality will be lower but if it saves a few dollars and doesn't deliver horrid quality I would be fine with it.
All DSLRs will record some compressed audio format. The audio you hear on a DVD in 16bit/48kHz.
If you plug the mic straight into the camera you will have minimal control and no way to monitor the audio as you shoot. You do want to hear the audio, don't you? To at the least make sure that it was recorded?
The audio quality of a DSLR is about two steps above a childs toy. Granted that there are some pretty cool childrens toys around these days, but nothing even close to DVD quality.
BTW, there are devices that record usable audio into DSLRs, however, they are actually more expensive than most micro-budget audio recorders, require an extra audio editing step, are not 100% reliable, and you still cannot hear the actual recorded audio.
And if the difference is specifically due to it being separate from the video when editing couldn't the audio simply be removed from it and then replaced as its own file to allow the same editing abilities during post?
When you shoot you slate each take visually and verbally - "Scene Four, Take Three" - SMACK!!! Once you have downloaded the video and audio files you need to line up the audio files with the video files. Tedious, but straight forward. Having the guide track from the camera makes it much easier than if you were working with film. Yes, you can partially automate the process with a software like PluralEyes. Once you've synced all of the audio to the video you can start editing. Consider it a first look at the footage.
I would recommend that you watch and LISTEN to about 50 indie shorts. What sets the good projects apart from the bad ones, at least on a technical level, is the quality of the audio. Quality audio starts on the set - choosing the correct mic for the location, using that mic properly, and recording in an uncompressed format. You do everything that you can to avoid the hollow roomy sound so prevalent in indie films.
Your project will only look as good as it sounds because "Sound is half of the the experience."