There is no side effect on difficulty due to mining empty blocks.
The simplest way to understand this, is that pools that do mine empty blocks do not have higher luck than pools that
don't mine empty blocks.
Mining empty blocks does not increase your luck and conversely,
NOT mining empty blocks does not decrease your luck.
If a pool didn't get a certain block due to do
NOT mining empty blocks, it doesn't mean they get less blocks, it simply means they get 'other' blocks instead.
Block finding luck has no predictable effect from the transactions you put in a block.
The two, and obvious, side effects are:
1) Less rewardLess reward is the obvious one: the pools that
don't mine empty blocks will get more reward in the blocks they find shortly after a network block change.
As the block reward halving makes the block rewards smaller, the effect of mining empty blocks becomes worse for those mining empty blocks.
Early in the year, when block rewards were very high, pools mining empty blocks where throwing away a large % of the possible BTC they could get in each empty block they mined.
In the last 60 blocks right now, I see 6 blocks by Antpool that are empty.
Clearly the people that mine there have no idea about this or really don't care
2) Longer confirm timesLonger confirms are a result of: those transactions that should have been included in the next, but empty, block are delayed at least an extra block.
The amount this affects the Bitcoin network depends on how full blocks are.
For the past few months blocks haven't really been all that full, so the side effect has been minimal.
Again, early in the year, when blocks rewards where very high due to lots of transactions, the transaction backlog was noticeably affected by empty block mining - each empty block meant thousands of extra transactions delayed due to no new transactions being confirmed in those empty blocks.
But the bottom line is that most people who mine are either ignorant of the situation (and typically ignorant of a very large part of what Bitcoin is all about and how it works) or don't care that they make less.
All the largest pools mine empty blocks: Antpool, Slush, BTC.com, BTC.TOP, ViaBTC, F2Pool, Poolin etc.
Fortunately, as the block reward gets smaller, it becomes more apparent, and some of those who actually prefer to be rewarded more, will shift away from these crappy pools that mine empty blocks.
However, most wont, since they are truly ignorant of their situation or don't care do anything about it if they do know, they simply see the $ they make, not the $ they're losing due to their stupidity.
This is clearly apparent due to the fact that most of these large pools charge
MUCH higher fees, yet the miners don't mind paying these
MUCH higher fees.