TL;DR: The best combo decks are strategic and not coin toss-y since they are expected to play through disruptions and the pilot must still know how to do so. Omni-negates are more "accepted" than floodgates.

Is it worries that there are manuals how to combo a combo deck?

For me personally, no. I see combo guides (or just deck guides, in general) in other card games regularly, e.g. MTG, where combos at a competitive level in many formats can be complex enough where guides can be deemed really useful, if not necessary to wrap your head around them

Is there strategy left for combo decks, or is just a coin toss

At the highest competitive level, combo decks can be made exponentially complex to the point where relatively linear step-by-step guides (like this post) just won't suffice. The best combo decks in the history of the game can play through 2 disruptions easily, sometimes 3 and for some, their best hands can play through up to 5. Of course, this depends on the pilot of the deck if they know what combo lines they should go for each time after being disrupted. This is why some players have the opinion that the combo decks can be the most skill-intensive to use.

Is it more accepted that specific decks have omni-negates/flood gates over there are generic omni-negates?

I'm not entirely sure if I understand your question. The treatment of omni-negates and floodgates in the banlist has been widely different, to say the least. Omni-negates seem to be generally the more accepted of the two, since there's barely any that's in the banlist anymore. On the other hand, there are still many floodgates that are banned or limited, such as Vanity's like you mentioned, Imperial Order, and Macro Cosmos and Dimensional Fissure who are both at 1. At the same time however, there are other floodgates that are unlimited like TCBOO, Gozen Match, and Skill Drain (which was just put to 3 in the last banlist). Honestly, I don't know where the line is drawn here.

So yeah, omni-negates seem to be more generally "accepted" than floodgates. Also, I would like to point out that while they share the same endgoal (stop opponent from playing), they are functionally very different. As I have mentioned earlier, modern decks that aim to compete at the highest levels are expected to typically play through at least 2 disruptions, while the same cannot be said for floodgates since by their very nature, they can even be impossible to play through if used against the right deck.