I have a Nexus 6.
The smaller rings (v1ntage/signature) do not reliably read at all for me with it.
The alpha reads reliably without a case. It will not read reliably with a case on (but will with a ring-size whole cut over the hot-spot).
I do not believe my Nexus 6 has faulty or abnormal NFC hardware. It reads credit cards and the mifare tags I have as reliably as any other phone I've tried.
I have done this on an Android Lollipop (5.0) device. There is no Xposed for 5.0 yet, so the options for disabling the sound are limited. I did it by editing the NFC apk. There are pitfalls to this method; here is how I did it. It requires root, a working adb setup, and some familiarity with the commandline.
Some warnings:
1 - it's really easy to screw up your phone and make it unbootable by doing this stuff. it's at your own risk.
2 - having nfc enabled with sounds is a security risk. don't do it unless you understand the disks.
Anyway:
1 - Take a full nandroid backup of the phone in case I screw up and and ruin it.
2 - On my computer, "adb pull /system/app/NfcNci/NfcNci.apk".
3 - unzip the apk file on my computer and replace the .ogg files inside it with a .ogg file of silence. Mine is https://www.dropbox.com/s/8vechle3xf4re1w/silent.ogg
4 - re-pack the apk file with zip. Note that the .ogg files within it have to be "stored" rather than "zipped" (ie uncompressed) otherwise the app won't work. I just made the whole file uncompressed (with "zip -0") - the increase in size is only about 500k anyway.
5 - adb push the new file on to the phone. It can't be pushed straight in to /system/app - so push it to the sdcard ("/storage/emulated/0/" or whatever)
6 - adb shell and su. As root, "mount -o remount,rw /storage)", copy the file that just got pushed over from the sdcard over the top of the existing /system/app/NfcNci/NfcNci.apk. Remove the odex for it in /system/app/NfcNci/
7 - reboot the phone.