What is a Hiden Jutsu?
Hiden (秘伝, Literally meaning: secret tradition) or simply "secret" techniques are passed down orally from generation to generation in certain regions or clans.

The groups who possess these techniques are usually extremely secretive about them in order to ensure that no one other than the members of the group or clan learn them. As such, they are passed down through oral means instead of being written down or recorded. A few hiden techniques require a special ability or lineage and as such are usually the pride and fame of the clan that possesses them. The Nara clan's Shadow Imitation Technique and the Aburame clan's Parasitic Destruction Insect Technique are examples of this. These techniques also cannot be copied through any means of simple observation.

They are not to be confused with kekkei genkai, as technically, hiden techniques can be taught to anyone.

How many clan currently have secret technique?
Only Few
Most of the clan have Chakra Nature as their ideal jutsu
How can this be pass down to players or members of this clan?
Personally I dont know but maybe in the character creation you could press a clan and gain the abilities or when you spawned and a member of the clan you will instantly learn the jutsu's?
@Vreg please answer or other persons who can answer

Clan jutsu:
Member finds a jutsu scroll, use it and then share it with his clan members.
If I recall correctly that's one possibility, might be mistaken of course.

A question then: In order to learn said jutsu, you 'have' to read the correlating scroll? So in theory then, one village could fight the others, obtain all the scrolls, and then...?

The jutsu scroll is defended by the clan that owns it, if you lose it that's your own fault.
I wasn't talking about the general scrolls, I was talking about the scrolls that could be found around the world. (If we're still using that system.)
So I would guess clans would hide it somewhere rather than having it out in the open.
 
If my memory serves me right, after using / learning from a scroll it becomes unusable, however you can copy some jutsus (as long as they're not forbidden jutsus, as those can't be copied.)
If you don't leave that many of those copied scrolls lying around, and just copy them when needed the chance of losing it should be much smaller (?) at least that's how I would see it.

Disclaimer:
I wrote down what I think / recall, without actually checking it with the devs.
Feel free to point out my mistakes / add on information if you know more about it.

Then all you would have to do to learn a clan's secret jutsu is create a new character. How secret is that?

Meant, if the clans and jutsu are listed in charrie creation, one can find out which jutsu belongs to each clan by making a new charrie. Plus ppl have more than one charrie slot, so if one is open they can just scan through the clans to refresh memory on who uses what. The only way to prevent that is to have clans listed, but not their jutsu. The secret scrolls will be found/claimed/hidden after the clan is formed anyway, so why would they be listed there. Trying to get across that having the secret clan jutsu listed with the clan choosing screens at creation would be defeating the purpose of a secret jutsu.

A better way is to let the clan teach members who meet whatever requirements clans set, someone who knows it will teach it to them. easy. done. also means that they should train with their clan in those jutsu. as the game advances obv ppl will make posts about special jutsu by clan ( which is dumb ) but it will happen, so those who look it up will be able to get a general idea of which clan has the cool jutsu anyway. like sharingan being known of at least far and wide outside its origination.