This is going to sound like an obnoxious answer (I don’t mean it that way), but the only real way to learn how to assess a threat is to get some experience.
For missions, there is EVE Survival:
This will give you detailed information on missions (damage profiles, enemy counts, etc.) and is extremely helpful for learning how to prepare for enemies.
There are many other kinds of NPC encounters in different environments like anomalies, combat sites, etc. and different regions have different kinds of pirates. That is far too detailed to get into here, but sources like E-Uni’s wiki can help there:
Search for a named site, pirate name, (or anything else, really) and this is as close to a “Manual for EVE” as there is out there.
Now, maybe a little more specific to your question, when you are just roaming around in space (and I’m assuming high sec here for simplicity), there are five main categories of rats that you might come across.
Normal rats. These will typically be groups of 1-3 ships. frigates and destroyers. Slow, very easy to deal with (but a step up from the tutorial Seekers). They will be the local pirate type (Serpentis in Gallente space, etc.). These guys will pop in every now and again in mining belts.
FOB rats. Be very careful of these. They will generally come in larger numbers than the standard rats and can hang around gates and stations in addition to dropping in on belts. These can be nasty since they are much more advanced and can call in other ships to help out. They are much harder to kill and are much better at killing you. You can check The Agency to see if there is a pirate FOB in the system you are exploring. If there is, it is a matter of time before these guys show up. Probably better to avoid the system until you get more confident (or at least better at avoiding them).
Incursions. You will know that an incursion is going on in a given system because there is an alert on screen, the visuals change, and you will suddenly have a new channel appear for you next to Local. Incursions are high-end PVE and are run by special fleets. These are very nasty rats and you are at extra risk because incursions also make your weapons and tank less effective. Generally best to avoid these systems.
Drifters. You will sometimes come across clusters of Autothysian Lancers hanging around gates or other celestial objects in certain systems. They will be red, but under most circumstances, will not attack you. Do not engage them. Not only will they put up a bit of a fight, but they can call in reinforcements that are extremely powerful.
NPC mining fleets. These are generally harmless, but if you attack them, they will also call in fairly powerful reinforcement fleets that can be pretty destructive. Also, if you attack the fleets repeatedly and you drop your standing with them, they may call in the reinforcement fleet when they see you instead of waiting for you to attack.
Now, more generally, you will learn how to spot these different NPCs and gain experience on how to deal with them (fight or flight). But, a huge part of the essence of EVE is unpredictability- and this is particularly true in PVP. You will rarely know what you are getting into, so you need to gain experience on how to manage fights and how to position yourself to bail out if needed. That gets into combat and flight tactics and is something you will learn after time. The short answer is learn how to see if you are holding up against the attack and know when it’s time to GTFO if you see things going south.
That said, push things and challenge yourself. Don’t just run away from the first shot (be it NPC or player)- hang in there and see how the fight goes while preparing to bail if you absolutely need to. Every fight you take leaves you better prepared for the next