I don't think there is another way but to use wire jumps to explicitely tell the reader that there is no connection on a crossing.
Sorry, you're wrong. The correct thing to do is the same thing everyone else on the planet is doing. This means, crossed lines without a dot are not connected, crossed lines with a dot are. That's the standard, that's what everyone does, so we do it also.
good:
| ----o---o----- |
bad:
| ----o-------- |
-Dan
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