Some meters will be damaged by trying thid but many are protected. A resistance measurement applies voltage across the leads and measures the voltage, doing an Ohm's law calculation to read resistance. It's still measuring voltage though, really... very low voltage but this circuitry usually has overvoltage protection.
A "short circuit" is a specific fault. It's common to call any electrical problem a "short", often incorrectly.
So what are your symptoms?
What is the battery voltage - key OFF, key ON but not running, idling, and above 3000 rpm? Best measured with a fully charged battery but useful info regardless.
If you can measure current at the battery with the same conditions that is very informative. If you disconnect the headlight, current should be safe for a 10A rated meter (common for cheaper digital meters) but DO NOT use electric start!
I am very leery of Li batteries in vehicles that were designed for Pb wet cells. Their charging characteristics are very different: the consequences of overcharge can be catastrophic, and full discharge will ruin them. Our bikes generally have less than excellent charging systems and no full discharge protection.
