There's no consistent way to be sure of whether you can scan something without using your scanner, but you can usually guess.
Sometimes a prompt to scan will show up in the lower left-hand corner of your screen. This shows up for many story scans, and a few non-story scans. There's a good radius on this so you're unlikely to miss something with the prompt, but most things have no prompt. Other than story scans, the most common time this shows up is near a certain type of object that I don't have a great term for. They have names like "Integrated Initiative Core Tech", and give you over 100 research credits for each one you scan.
Knowing When You Can Scan
Without your scanner out, you can guess whether you can scan something more often than not. Most of the time, scanning something with an identical appearance to something you've already scanned will not give you any additional research credits. The main exception to this are the high-output research items mentioned above. Thankfully, these come with a scan prompt.
So, generally, you don't need to bother scanning things if you've already scanned something that looks like it. This means you should get out your scanner and check new things.
With your scanner out, there are multiple cues indicating whether you can scan something, but not whether it will give you research credits or not. Within a certain range, anything scannable will be highlighted in a bright red. This is not ideal, as sometimes things in the environment which are already red will appear scannable but aren't. If something has already been scanned, it won't be that bright red color, and there will be a description on the right. If something has not already been scanned, there will be a distinctive beep when your reticle passes over it. This is different than the beeps from changing hazard levels, successfully scanning something, or closing the scanner.
You can scan things from decently far away. I haven't tried to scientifically measure it yet, but it's longer than the length of most normal rooms. Maybe 20 yards. This means you can check large areas for anything scannable from a single spot, rather than having to walk around the whole place with your scanner out.
Having your scanner out makes you slow and is kind of annoying, in my opinion. So, I try to avoid having it out if I can.
When you enter a new area, if there's anything that looks like it even might be new, whip out your scanner. Quickly sweep the area. If you hear any of the appropriate beeps, or any bright red jumps out at you, then slow down, go back, and check if there's something you can scan. If it's a large area, or has spots around corners with no line of sight from your current location, then you may need to move a ways and get the scanner back out to finish it off.
If a scan prompt shows up, whip out your scanner and do a 360. If you don't hear any beeps, it's probably on a different floor or the other side of a wall.
If you think something should be there, and can't find it, just walk around with the scanner and slowly check everything.