Just if you drilled a pencil-sized hole all the way through the lynx so attach a long screw and nut for mounting an accessory, so you think that would negatively affect the kayak in any way?  Aside from warranty and resale issues.  

Probably not if you did it correctly. But I still wouldn't personally, I would try to figure out a different solution even if convoluted. 

I've got tons of holes in my kayak.  Be sure to seal it up with something like Marine Goop, so water doesn't seep in, if you do that.  You can always reverse a hole in those plastic boats with a bit of extra plastic and a plastic welding iron (or low wattage soldering iron).  Just be sure to use the same plastic, typically HDPE in these cases. 

 

Though, unless you're mounting a really heavy accessory, I'd consider looking at pop rivets or well nuts.  That way you don't have to go all of the way through and risk a water leak.    

What are you mounting?

 bixpy motor.  the battery paavo has 4 holes that would be great to mount to a screw coming through the hole of the kayak.  very easy to remove quickly for charging but laps then secure for use on the water because the lynx is a very flat and open deck

can't you use the holes for the power anchor?  the threaded holes?

     Yes, I do think it would negatively effect the kayak. The Lynx is different then the Roto-molded kayaks. It is a solid cored foam filled kayak that has a thermo-formed plastic skin.  You'd be drilling a hole through the foam core and over time it might either break down or get waterlogged.  I think you could used some type of Polyurethane adhesive or West Marine G-Flex epoxy to glue a T-track or two or block/s that you could screw into for a couple of pad eyes or straps to hold the battery in place.

     Might check with Hobie or the place you bought it from or if you've got a full service kayak dealer that knows what they are doing.

Good Luck,

Fishingmickey

 

i have a power pole mounted in the holes already.  i’m thinking of just getting a stronger plastic bin and 3M mounting the bin as a container with maybe some bungees to keep it secure.  

If you’re talking about a crate you could just strap it with two cam straps all the way around the boat. Then no drilling or gluing required.