Don't worry about navigation links. Since they're repeated on EVERY page, Google has learned to pretty much ignore them. They know they're useful for the client, and they know that these are what you consider the "most important" pages in your site, but the real focus is on context links. These are where the real actions happen.
The Silo structure has been around for a very long time, and if you look at libraries, they're built just like a Silo. Want to know about Religion, all those books are in this corner. Want to know about fiction, they're all over here. Your website can be built in the same fashion.
Everything related to dogs is going to be linked from the DOG page. Then a user has to click to a category for "small dogs" and then get into the drilldown list for "small dog toys" and then drill another level for "pastic toys". At that point, you may have lost your user as you exceeded the "3 clicks or less" rule.
3 clicks or less
<- been around a while, but I *LIVE & TEACH * by this rule. It's just plain common sense.
If a user can't find what they want in 3 clicks, you stand a VERY high chance that they will go back to Google and search again.
So, going back to Silo Structure, it does work, and it helps for organization, but when it comes to optimization you don't want people to land on the "dog" page. You want google searchers to land on "plastic chew toys".
Here's the site structure (breadcrumbs or trail of crumbs);
home > dogs > small dogs > toys > plastic chew toys > Awesome #1 toy
You want the user to land on the "Awesome #1 Toy" page and not have to go through the categories or structures.
In traditional Silos, you'd be advised to link the "Awesome #1 Toy" to each of the categories above it, or maybe just the "dog" category, which would then in theory boost the Dog page as it has so many internal links pointing to it that it must be important.
As long as each page is linked to whatever the topic is about, Google is going to figure it all out for you. You no longer need to be overly explicit. If anything, having tons of links will confuse your user, and thus you get dinged by Google for a bad user experience
Over optimization is a pretty real thing, but you have to really go out of your way to land in a penalty situation.
Your competitors may be outranking you, not because of optimization, but because of the links they actually have and the authority they have in an industry.
When we provide consulting, one of the things we continue to repeat to clients is "Keep an eye on the competition, but FOCUS on your business.
" If you spend all your time watching what the competition is doing, you'll often miss the mark in how awesome YOU are and why you're better.
Perform your base optimizations, and then take inventory of what you've done. Run an audit, audit the competition, evaluate and improve again.