1) Are there consequences for your average farmer not answering a call to arms? How would you even know if he didn't come? Could you pay a lump sum to get out of military service? Does everyone that is conscripted have to sign a contract? If two kingdoms go to war and you really think about it, it's an absolute nightmare logistically speaking. You have to gather the troops, mass supplies, be able to move those troops and supplies across a hostile land while most likely under constant harassment. I would suspect a kingdom would lose a lot of soldiers and supplies on their campaign. How would desertion work? Are there any game mechanics tied to this or is it all player driven? Meaning if someone deserts, is there a way for them to be flagged as a criminal?
2) Also all of the questions above apply to NPC's and OPC's. How do they interact with all of this?
3) Lets say i'm a count and I have an average amount of land and a average amount of inhabitants. How many soldiers could I expect to realistically raise for a planned offensive war? Also in my average city as a count how many guards could I expect to patrol my streets and personally guard me? Same questions for mayors and barons.
For these, we can do some logicks.
1) The consequences would vary from county to county, or duchy or kingdom depending on how laws are set up. Maybe merchants and smiths are exempt and can pay their way out in exchange for supplying the army with something. Same thing with a lump sum, you pay to get out of it, but at a certain point, you may run out of mercenaries and need more soldiers.
If you're a smart count, I would make sure you a) have militias regardless of if you are on the border or not and b) keep lists of their names, towns, occupations etc. and simply do roll calls. Otherwise it would be to expensive for you top have people hired to make sure all the militias muster completely.
The contract would likely be implicit, we all have obligations to our lords. Unless you set up your law to require a specific contract, guaranteeing pay or equipment etc. for a militia or conscript.
Wars are indeed a logistical nightmare, most have been won or lost due to that fact.
Desertion would be player driven, coming back to the implicit or explicit contract. As count, you would be able to flag deserters as criminals the same way as anyone else who breaks a law. Keeping track of militia/conscripts members and their statuses (KIA, MIA, etc.) would also help.
2) NPCs and OPCs act similarly, but NPCs are very different from OPCs. We'll have to wait and see, but most contracts are do this in exchange for this. So OPCs may be able to muster or something like that if prompted. But we'll have to wait for testing on that.
3) If it's a planned Offensive it would depend on your preparations. But I would, upon launch, maybe do a census, figure out how many people you have, where they work etc. and ask employers the minimum amount of people they need to run their shops etc. And go from there. As for guards, the town guards and your personal guards are likely different groups unless you keep them the same. But that simply depends on how many you hire/can afford. As a count, probably more than a Baron or Mayor, who may simple have a bodyguard or two.