My pannier arrangement is such that the front panniers contain valuables, tools, quick-access clothing, and all the food stuff. Which covers most of what I'm likely to want access to during a shorter ferry crossing, and (with the exception of fuel bottle mounted on the bike[1]) anything security are likely to be interested in.
The big panniers with tent, sleeping bag/mat, spare clothing, wash things, etc. stay on the bike. Unless it's an overnight sailing where I'd go to the effort to bring all four to the cabin so I have access to the extra clothes and wash things. I'll also not bother removing pump, lights, etc.
Security (looked like army types, rather than customs) were actively searching vehicles when I went through Dunkirk a couple of years ago. They complimented my usual bike and waved me through. I think they're more interested in hidden humans than penknives etc.
[1] Seems likely that if a sniffer dog is going to get interested in something, it's going to be this, and having it exposed saves having your panniers explored. Not sure what the actual rules on alcohol/paraffin/LPG/etc are, but I expect the law of unusualness means that half a litre of meths is an explosion risk that will kill everyone utterly to DETH, but petrol-fuelled vehicles with hot engines and active electrical systems are completely harmless.