Is it possible to tell calibre lvs to not perform deep short?

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I don't think so. Calibre basically doesn't support feedthrough nets -- if two top-level ports are connected by a long wire Calibre will totally ignore the wire resistance. The only way around this is to actually change your both your layout (ugh!) and schematic -- you have to remove the wire from your layout, replace it with the special "metal-resistor" layer, and then put an explicit resistor in your schematic to prevent LVS from failing.

If the ports aren't top-level ports it will do the right thing, but this different treatment for top-level ports versus non-top-level ports really wrecks hierarchical approaches to managing complexity.
 
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