I'll get to some specifics about what you're asking, but first I want to offer some friendly advice: if you don't know the answers to simple questions like this then you shouldn't be considering an online-multiplayer RPG as a project. What you're talking about is RPG game systems 101 and it goes all the way from basic pen & paper systems to complex MMORPGs.
Frankly, you're not ready if you don't already know the fundamentals inside and out. I would strongly suggest you spend some time as a GM/DM for a pen & paper group and learn a number of big systems (D&D, 5 Rings, White Wolf, etc) until you understand not only how they are different but why.
To give you some help here are a few thoughts:
1) You're focusing too much on specifics and not enough on the underlying design principles. It doesn't matter if you have a damage type called "Magical" because that's just a descriptive name, what matters is how it's implemented and what differentiates it from other damage types.
For example, what makes Ice different from Lightning? In most systems it's that ice has some form of cold/chill/freeze effect and lightning has some form of shock/stun/chain effect. Those characteristics are then what guide you to design the skills/spells/auras/etc that use those elements. An ice spell could shatter and slow enemies, a lightning spell could shock and interrupt attacks, a poison spell could cause confusion and lead to less accurate attacks, etc. It's whatever YOU decide.
2) Don't confuse damage effects and damage types. The former is how damage is applied (up front, over time, after a delay, etc) and the latter is what kind of damage is applied. When you look at most RPG systems a "Bleed" is typically a damage effect (DoT) and so also needs to be given a damage type (Physical).
Poison is a bit different because some games use it as both, but I would strongly suggest that you refrain from doing that. It's confusing and ultimately doesn't gain you anything, so I would choose one or the other and design around that decision.
3) Having a "base" damage category (Physical, Magic, etc) is fine from a design perspective, but I would advise you to NOT allow attacks/weapons/stats to directly impact or use the base category if you go that route because it will create an absolutely nightmare for damage/mitigation balance.
Let's say you have a "Magic" category containing 4 damage types (Magic, Ice, Fire, Chaos). If you allow a weapon to do "Magic" damage then it will either be garbage or overpowered depending on whether elemental damage and resistances "double-dip" or not. Here are a few potential pitfalls:
- How is mitigation determined for both elemental and base magic damage?
- Do you derive magic resistance from base stats, from item stats, or both?
- Does magic resist also effect elemental resist and if so is it additive, multiplicative or added separately? If separately is it mitigated first and how does that impact the second calculation?
- How is damage increased and is it handled the same way as resists? (All the same questions apply)
For example, look at Diablo 3's resistance system where you have "all resist" and individual resistances. Ask yourself: what is the purpose of individual resistances in D3 and are they effective? The answer is no, they are completely pointless because they are completely outclassed by all resist in every way.
Why? Here are a few reasons:
- The resistances aren't even remotely balanced, physical is far better than the elemental resists.
- You can gem for All Resist but not for individual resists.
- You can't gain adequate resists across the board with individual resists.
- The play-style of the game relies on avoiding damage more than mitigating it.
I could continue, but the point is that individual resists don't serve any practical purpose in the game. Just like the other pointless secondary stats like chance to fear on hit, and basically every gem that isn't main-stat or all resist. D3 does a lot right, it's gem and mitigation system are two things that aren't done well at all.
This is getting long so I'll wrap this up by offering a couple suggestions:
1) Design your classes or builds around the type of play-style you want to enable and not the type of damage they do. Once you've figured out those then it's a lot easier to figure out the damage types.
2) When creating your damage types: KEEP IT SIMPLE. You don't need to allow for every single possible combination, frankly games that try to do that inevitably fail... either because the systems don't work, are extremely boring because everything is homogenized, or because they offer the illusion of choice but have no actual substance.
3) Stick to the classics. Having both non-magic and magic damage types are important, but make sure they are relatively even in power when compared with how hard/easy it is to mitigate those damage sources. Also, make sure each damage type has a clearly defined purpose or play-style, don't add things just for the sake of variety. You're better off sticking with fire, ice, lightning and making them unique than adding water, air, earth, dark, light, holy, chaos, poison... and having them all be clones.
Good luck :P