There are plenty of good reasons to run a server-side ethereum connection. If you want to do so:
install web3 directly. Embark has it's own version of web3, but I found it easiest just to install it local to my site
npm install web3
Instantiate Web3 in your node.js script
var Web3 = require('web3'); web3 = new Web3(new Web3.providers.HttpProvider("http://localhost:8545"));
Copy/link your dist/contracts folder somewhere accessible to your site. Then import the json for the contract you wish to interact with:
sc_abi = require('./contracts/<YourContract>.json');
Finally, instantiate a web3 object and away you go...
MyContract = new web3.eth.Contract(sc_abi.abi, sc_abi.address); MyContract.methods.getMyBalance().call().then(...)
DApps are meant to be client side only, the dev webserver of embark is there as a convenience to easy access the dapp for development purposes. You can put the dapp anywhere: in your own webserver, ipfs and even distribute it as a zip file since the dapp can be even open directly in the browser as a file.