Weird, that doesn't happen to me.
Can you check the 'nohud' setting on the energy bar in the config ? It should be false.
The config is in %appdata%/SpaceEngineers/Storage/428842256_Helmet/helmet.cfg
You can just copypaste this in your text editor's open dialog and it should open that file.

The drill's position is screwed up, it's way too close to the screen to the point that it's clipping which renders it above the HUD, that will probably be fixed by the devs.
I think I can also fix it myself temporarily until they fix it.

And sadly no, I can't make the GPS markers show when you have the vanilla HUD turned off.

Well, it was simple enough to move the drill, I've also moved the assault rifle a bit and tweaked the arm on the grinder because it was really awkward, just updated the mod with these changes.

Ah, I loaded an older survival world and I can see the energy bar being hidden with the vanilla HUD on and shows with the HUD off for some reason, so I have the issue replicated, now on to fixing it xD

EDIT: Hmm, seems that the nohud setting for that was set to True in the config because of a typo xD gah, no idea how to apply this to everybody without making them change it manually... I guess I can rename it.

EDIT #2: Well, I replaced it with 'hudmode', the old setting is removed automatically since it doesn't exist and the new one has more features :}

well, thanks alot again! I got to the same conclusion, the setting was set to True for one of the elements, changed it back to false.

Thanks again sir :)

In relation to the GPS waypoints. There is a mod:
http://steamcommunity.yuanyoumao.com/sharedfiles/filedetails/?id=363037395
I haven't tried to see if it solves your problem. I will do some testing and report back.

EDIT: Tested. It also goes away with the vanilla HUD. I'm looking into it.