Since you are talking of word documents, I assume, you are using it on Windows. Some of the smartcard or USB Token drivers, on Windows OS (as far as I know), has feature to save or remember user PIN. Enabling that feature would prevent asking for PIN for every cryptographic operation.
If driver does not have such feature, then you may have to study and use CSP (Crypto Service Provider on Windows) of the device if available or use direct PKCS#11 API to achieve the operation by providing PIN programmatically, but these things requires sufficient expertise and understanding of PKI.
For bulk signing of pdf there are lot of free and paid softwares available which provides you lot of automated features. You may consider going for once instead of re-inventing the wheel. My Co. CISPL also provides Signer.Digital range of solutions for achieving the task.
与恶龙缠斗过久,自身亦成为恶龙;凝视深渊过久,深渊将回以凝视…